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Opened 81 minutes ago
#19763 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.7.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003969bb000 (most recent call first):
File "/Applications/ChimeraX-1.11.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000003959af000 (most recent call first):
File "/Applications/ChimeraX-1.11.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000003949a3000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX-1.11.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000393997000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000039298b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000039197f000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000390973000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000038f967000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000377e33000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000376e27000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x00000003737df000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000361e27000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000035e307000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000032addb000 (most recent call first):
File "/Applications/ChimeraX-1.11.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000329dcf000 (most recent call first):
File "/Applications/ChimeraX-1.11.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000031ab03000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX-1.11.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000319af7000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000318aeb000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000317adf000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000316ad3000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000315ac7000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000314abb000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000313aaf000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000312aa3000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000311a97000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000310a8b000 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x000000020cb66200 (most recent call first):
File "/Applications/ChimeraX-1.11.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.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.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, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PIL._imaging, 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.pdb._pdbio, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp, kiwisolver._cext (total: 53)
{"app_name":"ChimeraX","timestamp":"2026-01-22 19:42:39.00 +0800","app_version":"1.11.0","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.7.2 (24G325)","roots_installed":0,"name":"ChimeraX","incident_id":"87870615-ED77-4B6C-89CF-5B3DF26581E9"}
{
"uptime" : 270000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,12",
"coalitionID" : 21653,
"osVersion" : {
"train" : "macOS 15.7.2",
"build" : "24G325",
"releaseType" : "User"
},
"captureTime" : "2026-01-22 19:42:31.3966 +0800",
"codeSigningMonitor" : 2,
"incident" : "87870615-ED77-4B6C-89CF-5B3DF26581E9",
"pid" : 69363,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-01-21 15:23:58.4092 +0800",
"procStartAbsTime" : 5557025869937,
"procExitAbsTime" : 6600115373256,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.0","CFBundleVersion":"1.11.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"99698E01-9E64-54C1-A053-EE6DB830EF2F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A249799F-0BC7-E8C6-07F0-88FFA016A535",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["regionIneligible","countryBillingIneligible","countryLocationIneligible"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
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"uuid" : "63a54ce1-2ab6-3673-82e4-d8489d811475",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
}
],
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"base" : 6953500672,
"size" : 5039669248,
"uuid" : "b395a5f6-c55f-3776-8d60-908ce43d7959"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)
Writable regions: Total=3.6G written=48.8M(1%) resident=2243K(0%) swapped_out=46.7M(1%) unallocated=3.5G(99%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 1024K 8
Activity Tracing 256K 1
CG image 2304K 43
ColorSync 800K 39
CoreAnimation 6416K 146
CoreGraphics 48K 3
CoreImage 160K 5
CoreUI image data 4384K 33
Foundation 48K 2
Kernel Alloc Once 32K 1
MALLOC 2.5G 113
MALLOC guard page 288K 18
Mach message 64K 2
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 1232K 77
Stack 646.5M 78
Stack Guard 56.0M 1
VM_ALLOCATE 305.6M 348
VM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)
__AUTH 5523K 697
__AUTH_CONST 77.4M 944
__CTF 824 1
__DATA 33.5M 1073
__DATA_CONST 53.5M 1092
__DATA_DIRTY 2777K 342
__FONT_DATA 2352 1
__GLSLBUILTINS 5174K 1
__INFO_FILTER 8 1
__LINKEDIT 647.8M 142
__OBJC_RO 61.4M 1
__OBJC_RW 2396K 1
__TEXT 1.3G 1085
__TEXT (graphics) 6656K 27
__TPRO_CONST 128K 2
dyld private memory 1840K 17
mapped file 1.0G 235
page table in kernel 2243K 1
shared memory 3824K 32
=========== ======= =======
TOTAL 6.8G 6620
TOTAL, minus reserved VM space 6.7G 6620
",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "d29d948b870d742c600c8fb68978b398db79b540",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "67d07cd6a7affa169ae21f45",
"factorPackIds" : {
},
"deploymentId" : 240000002
},
{
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/wendyk/Downloads/top_preds/complex.1.pdb
Summary of feedback from opening
/Users/wendyk/Downloads/top_preds/complex.1.pdb
---
warnings | Ignored bad PDB record found on line 1
ATOM 1 N SER A 100 31.509 17.900 8.558 2 1 1.63 -.15
Ignored bad PDB record found on line 2
ATOM 2 CA SER A 100 31.532 16.403 8.433 2 1 2.03 .10
Ignored bad PDB record found on line 3
ATOM 3 C SER A 100 32.006 15.864 7.092 2 1 1.67 .60
Ignored bad PDB record found on line 4
ATOM 4 O SER A 100 32.000 16.589 6.101 2 1 1.38 -.55
Ignored bad PDB record found on line 5
ATOM 5 N PRO A 101 32.436 14.584 7.051 3 0 1.63 -.25
2135 messages similar to the above omitted
> open /Users/wendyk/Downloads/top_preds/complex.1.pdb format pdb
Summary of feedback from opening
/Users/wendyk/Downloads/top_preds/complex.1.pdb
---
warnings | Ignored bad PDB record found on line 1
ATOM 1 N SER A 100 31.509 17.900 8.558 2 1 1.63 -.15
Ignored bad PDB record found on line 2
ATOM 2 CA SER A 100 31.532 16.403 8.433 2 1 2.03 .10
Ignored bad PDB record found on line 3
ATOM 3 C SER A 100 32.006 15.864 7.092 2 1 1.67 .60
Ignored bad PDB record found on line 4
ATOM 4 O SER A 100 32.000 16.589 6.101 2 1 1.38 -.55
Ignored bad PDB record found on line 5
ATOM 5 N PRO A 101 32.436 14.584 7.051 3 0 1.63 -.25
2135 messages similar to the above omitted
> open /Users/wendyk/Downloads/top_preds/complex.1.pdb format pdb
Summary of feedback from opening
/Users/wendyk/Downloads/top_preds/complex.1.pdb
---
warnings | Ignored bad PDB record found on line 1
ATOM 1 N SER A 100 31.509 17.900 8.558 2 1 1.63 -.15
Ignored bad PDB record found on line 2
ATOM 2 CA SER A 100 31.532 16.403 8.433 2 1 2.03 .10
Ignored bad PDB record found on line 3
ATOM 3 C SER A 100 32.006 15.864 7.092 2 1 1.67 .60
Ignored bad PDB record found on line 4
ATOM 4 O SER A 100 32.000 16.589 6.101 2 1 1.38 -.55
Ignored bad PDB record found on line 5
ATOM 5 N PRO A 101 32.436 14.584 7.051 3 0 1.63 -.25
2135 messages similar to the above omitted
> open /Users/wendyk/Downloads/top_preds/complex.1.pdb format pdb
Summary of feedback from opening
/Users/wendyk/Downloads/top_preds/complex.1.pdb
---
warnings | Ignored bad PDB record found on line 1
ATOM 1 N SER A 100 31.509 17.900 8.558 2 1 1.63 -.15
Ignored bad PDB record found on line 2
ATOM 2 CA SER A 100 31.532 16.403 8.433 2 1 2.03 .10
Ignored bad PDB record found on line 3
ATOM 3 C SER A 100 32.006 15.864 7.092 2 1 1.67 .60
Ignored bad PDB record found on line 4
ATOM 4 O SER A 100 32.000 16.589 6.101 2 1 1.38 -.55
Ignored bad PDB record found on line 5
ATOM 5 N PRO A 101 32.436 14.584 7.051 3 0 1.63 -.25
2135 messages similar to the above omitted
> open /Users/wendyk/Downloads/top_preds/complex.2.pdb
Summary of feedback from opening
/Users/wendyk/Downloads/top_preds/complex.2.pdb
---
warnings | Ignored bad PDB record found on line 1
ATOM 1 N SER A 100 31.509 17.900 8.558 2 1 1.63 -.15
Ignored bad PDB record found on line 2
ATOM 2 CA SER A 100 31.532 16.403 8.433 2 1 2.03 .10
Ignored bad PDB record found on line 3
ATOM 3 C SER A 100 32.006 15.864 7.092 2 1 1.67 .60
Ignored bad PDB record found on line 4
ATOM 4 O SER A 100 32.000 16.589 6.101 2 1 1.38 -.55
Ignored bad PDB record found on line 5
ATOM 5 N PRO A 101 32.436 14.584 7.051 3 0 1.63 -.25
2135 messages similar to the above omitted
> open /Users/wendyk/Downloads/h-CLEC2.cif
h-CLEC2.cif title:
Crystal structure of human CLEC-2 (CLEC1B) [more info...]
Chain information for h-CLEC2.cif #1
---
Chain | Description | UniProt
A | CLEC1B PROTEIN | Q9P126_HUMAN 100-221
61 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show "Altloc Explorer"
> hbonds /A:105,111,124,138,141,145,164,168,184,209,218 & @@num_alt_locs>1
> interModel false reveal true name "altloc H-bonds" updateGroup true
30 hydrogen bonds found
> select /A:100-221
1021 atoms, 1053 bonds, 4 pseudobonds, 122 residues, 2 models selected
> select /A:100-221
1021 atoms, 1053 bonds, 4 pseudobonds, 122 residues, 2 models selected
> help help:user/tools/altlocexplorer.html
> select /A:100-221
1021 atoms, 1053 bonds, 4 pseudobonds, 122 residues, 2 models selected
> select /A:100-221
1021 atoms, 1053 bonds, 4 pseudobonds, 122 residues, 2 models selected
> undo
> hide #!1 models
> show #!1 models
> select add #1
1267 atoms, 1053 bonds, 30 pseudobonds, 368 residues, 2 models selected
> select subtract #1
Nothing selected
> nucleotides ladder
> volume style surface
No volumes specified
> ui mousemode right "delete markers"
> ui tool show "Model Loops"
Populating font family aliases took 157 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
No alignments chosen for modeling
> select add #1
1267 atoms, 1053 bonds, 30 pseudobonds, 368 residues, 2 models selected
> ui tool show "Model Loops"
No alignments chosen for modeling
> ui tool show "Model Loops"
No alignments chosen for modeling
> ui tool show "Model Loops"
> select subtract #1
Nothing selected
> ui tool show "Model Loops"
> select /A:100-221
1021 atoms, 1053 bonds, 4 pseudobonds, 122 residues, 2 models selected
> select /A:100-221
1021 atoms, 1053 bonds, 4 pseudobonds, 122 residues, 2 models selected
> show target m
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Model Loops"
> modeller refine 1/A:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
Webservices job id: BSNX1EVTJVV8PM1J
Webservices job finished: BSNX1EVTJVV8PM1J
Modeller job (ID BSNX1EVTJVV8PM1J) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 93, in
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 151, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 700, in _check_select_atoms
raise ModellerError("no atoms selected for optimization")
_modeller.ModellerError: no atoms selected for optimization
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
4.18.0-553.89.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2026/01/21 18:52:32
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 406977 397.438 0.388
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 408445 398.872 0.390
read_al_374_> Non-standard residue type,position,sequence: w 123 1
read_al_374_> Non-standard residue type,position,sequence: w 124 1
read_al_374_> Non-standard residue type,position,sequence: w 125 1
read_al_374_> Non-standard residue type,position,sequence: w 126 1
read_al_374_> Non-standard residue type,position,sequence: w 127 1
read_al_374_> Non-standard residue type,position,sequence: w 128 1
read_al_374_> Non-standard residue type,position,sequence: w 129 1
read_al_374_> Non-standard residue type,position,sequence: w 130 1
read_al_374_> Non-standard residue type,position,sequence: w 131 1
read_al_374_> Non-standard residue type,position,sequence: w 132 1
read_al_374_> Non-standard residue type,position,sequence: w 133 1
read_al_374_> Non-standard residue type,position,sequence: w 134 1
read_al_374_> Non-standard residue type,position,sequence: w 135 1
read_al_374_> Non-standard residue type,position,sequence: w 136 1
read_al_374_> Non-standard residue type,position,sequence: w 137 1
read_al_374_> Non-standard residue type,position,sequence: w 138 1
read_al_374_> Non-standard residue type,position,sequence: w 139 1
read_al_374_> Non-standard residue type,position,sequence: w 140 1
read_al_374_> Non-standard residue type,position,sequence: w 141 1
read_al_374_> Non-standard residue type,position,sequence: w 142 1
read_al_374_> Non-standard residue type,position,sequence: w 143 1
read_al_374_> Non-standard residue type,position,sequence: w 144 1
read_al_374_> Non-standard residue type,position,sequence: w 145 1
read_al_374_> Non-standard residue type,position,sequence: w 146 1
read_al_374_> Non-standard residue type,position,sequence: w 147 1
read_al_374_> Non-standard residue type,position,sequence: w 148 1
read_al_374_> Non-standard residue type,position,sequence: w 149 1
read_al_374_> Non-standard residue type,position,sequence: w 150 1
read_al_374_> Non-standard residue type,position,sequence: w 151 1
read_al_374_> Non-standard residue type,position,sequence: w 152 1
read_al_374_> Non-standard residue type,position,sequence: w 153 1
read_al_374_> Non-standard residue type,position,sequence: w 154 1
read_al_374_> Non-standard residue type,position,sequence: w 155 1
read_al_374_> Non-standard residue type,position,sequence: w 156 1
read_al_374_> Non-standard residue type,position,sequence: w 157 1
read_al_374_> Non-standard residue type,position,sequence: w 158 1
read_al_374_> Non-standard residue type,position,sequence: w 159 1
read_al_374_> Non-standard residue type,position,sequence: w 160 1
read_al_374_> Non-standard residue type,position,sequence: w 161 1
read_al_374_> Non-standard residue type,position,sequence: w 162 1
read_al_374_> Non-standard residue type,position,sequence: w 163 1
read_al_374_> Non-standard residue type,position,sequence: w 164 1
read_al_374_> Non-standard residue type,position,sequence: w 165 1
read_al_374_> Non-standard residue type,position,sequence: w 166 1
read_al_374_> Non-standard residue type,position,sequence: w 167 1
read_al_374_> Non-standard residue type,position,sequence: w 168 1
read_al_374_> Non-standard residue type,position,sequence: w 169 1
read_al_374_> Non-standard residue type,position,sequence: w 170 1
read_al_374_> Non-standard residue type,position,sequence: w 171 1
read_al_374_> Non-standard residue type,position,sequence: w 172 1
read_al_374_> Non-standard residue type,position,sequence: w 173 1
read_al_374_> Non-standard residue type,position,sequence: w 174 1
read_al_374_> Non-standard residue type,position,sequence: w 175 1
read_al_374_> Non-standard residue type,position,sequence: w 176 1
read_al_374_> Non-standard residue type,position,sequence: w 177 1
read_al_374_> Non-standard residue type,position,sequence: w 178 1
read_al_374_> Non-standard residue type,position,sequence: w 179 1
read_al_374_> Non-standard residue type,position,sequence: w 180 1
read_al_374_> Non-standard residue type,position,sequence: w 181 1
read_al_374_> Non-standard residue type,position,sequence: w 182 1
read_al_374_> Non-standard residue type,position,sequence: w 183 1
read_al_374_> Non-standard residue type,position,sequence: w 184 1
read_al_374_> Non-standard residue type,position,sequence: w 185 1
read_al_374_> Non-standard residue type,position,sequence: w 186 1
read_al_374_> Non-standard residue type,position,sequence: w 187 1
read_al_374_> Non-standard residue type,position,sequence: w 188 1
read_al_374_> Non-standard residue type,position,sequence: w 189 1
read_al_374_> Non-standard residue type,position,sequence: w 190 1
read_al_374_> Non-standard residue type,position,sequence: w 191 1
read_al_374_> Non-standard residue type,position,sequence: w 192 1
read_al_374_> Non-standard residue type,position,sequence: w 193 1
read_al_374_> Non-standard residue type,position,sequence: w 194 1
read_al_374_> Non-standard residue type,position,sequence: w 195 1
read_al_374_> Non-standard residue type,position,sequence: w 196 1
read_al_374_> Non-standard residue type,position,sequence: w 197 1
read_al_374_> Non-standard residue type,position,sequence: w 198 1
read_al_374_> Non-standard residue type,position,sequence: w 199 1
read_al_374_> Non-standard residue type,position,sequence: w 200 1
read_al_374_> Non-standard residue type,position,sequence: w 201 1
read_al_374_> Non-standard residue type,position,sequence: w 202 1
read_al_374_> Non-standard residue type,position,sequence: w 203 1
read_al_374_> Non-standard residue type,position,sequence: w 204 1
read_al_374_> Non-standard residue type,position,sequence: w 205 1
read_al_374_> Non-standard residue type,position,sequence: w 206 1
read_al_374_> Non-standard residue type,position,sequence: w 207 1
read_al_374_> Non-standard residue type,position,sequence: w 208 1
read_al_374_> Non-standard residue type,position,sequence: w 209 1
read_al_374_> Non-standard residue type,position,sequence: w 210 1
read_al_374_> Non-standard residue type,position,sequence: w 211 1
read_al_374_> Non-standard residue type,position,sequence: w 212 1
read_al_374_> Non-standard residue type,position,sequence: w 213 1
read_al_374_> Non-standard residue type,position,sequence: w 214 1
read_al_374_> Non-standard residue type,position,sequence: w 215 1
read_al_374_> Non-standard residue type,position,sequence: w 216 1
read_al_374_> Non-standard residue type,position,sequence: w 217 1
read_al_374_> Non-standard residue type,position,sequence: w 218 1
read_al_374_> Non-standard residue type,position,sequence: w 219 1
read_al_374_> Non-standard residue type,position,sequence: w 220 1
read_al_374_> Non-standard residue type,position,sequence: w 221 1
read_al_374_> Non-standard residue type,position,sequence: w 222 1
read_al_374_> Non-standard residue type,position,sequence: w 223 1
read_al_374_> Non-standard residue type,position,sequence: w 224 1
read_al_374_> Non-standard residue type,position,sequence: w 225 1
read_al_374_> Non-standard residue type,position,sequence: w 226 1
read_al_374_> Non-standard residue type,position,sequence: w 227 1
read_al_374_> Non-standard residue type,position,sequence: w 228 1
read_al_374_> Non-standard residue type,position,sequence: w 229 1
read_al_374_> Non-standard residue type,position,sequence: w 230 1
read_al_374_> Non-standard residue type,position,sequence: w 231 1
read_al_374_> Non-standard residue type,position,sequence: w 232 1
read_al_374_> Non-standard residue type,position,sequence: w 233 1
read_al_374_> Non-standard residue type,position,sequence: w 234 1
read_al_374_> Non-standard residue type,position,sequence: w 235 1
read_al_374_> Non-standard residue type,position,sequence: w 236 1
read_al_374_> Non-standard residue type,position,sequence: w 237 1
read_al_374_> Non-standard residue type,position,sequence: w 238 1
read_al_374_> Non-standard residue type,position,sequence: w 239 1
read_al_374_> Non-standard residue type,position,sequence: w 240 1
read_al_374_> Non-standard residue type,position,sequence: w 241 1
read_al_374_> Non-standard residue type,position,sequence: w 242 1
read_al_374_> Non-standard residue type,position,sequence: w 243 1
read_al_374_> Non-standard residue type,position,sequence: w 244 1
read_al_374_> Non-standard residue type,position,sequence: w 245 1
read_al_374_> Non-standard residue type,position,sequence: w 246 1
read_al_374_> Non-standard residue type,position,sequence: w 247 1
read_al_374_> Non-standard residue type,position,sequence: w 248 1
read_al_374_> Non-standard residue type,position,sequence: w 249 1
read_al_374_> Non-standard residue type,position,sequence: w 250 1
read_al_374_> Non-standard residue type,position,sequence: w 251 1
read_al_374_> Non-standard residue type,position,sequence: w 252 1
read_al_374_> Non-standard residue type,position,sequence: w 253 1
read_al_374_> Non-standard residue type,position,sequence: w 254 1
read_al_374_> Non-standard residue type,position,sequence: w 255 1
read_al_374_> Non-standard residue type,position,sequence: w 256 1
read_al_374_> Non-standard residue type,position,sequence: w 257 1
read_al_374_> Non-standard residue type,position,sequence: w 258 1
read_al_374_> Non-standard residue type,position,sequence: w 259 1
read_al_374_> Non-standard residue type,position,sequence: w 260 1
read_al_374_> Non-standard residue type,position,sequence: w 261 1
read_al_374_> Non-standard residue type,position,sequence: w 262 1
read_al_374_> Non-standard residue type,position,sequence: w 263 1
read_al_374_> Non-standard residue type,position,sequence: w 264 1
read_al_374_> Non-standard residue type,position,sequence: w 265 1
read_al_374_> Non-standard residue type,position,sequence: w 266 1
read_al_374_> Non-standard residue type,position,sequence: w 267 1
read_al_374_> Non-standard residue type,position,sequence: w 268 1
read_al_374_> Non-standard residue type,position,sequence: w 269 1
read_al_374_> Non-standard residue type,position,sequence: w 270 1
read_al_374_> Non-standard residue type,position,sequence: w 271 1
read_al_374_> Non-standard residue type,position,sequence: w 272 1
read_al_374_> Non-standard residue type,position,sequence: w 273 1
read_al_374_> Non-standard residue type,position,sequence: w 274 1
read_al_374_> Non-standard residue type,position,sequence: w 275 1
read_al_374_> Non-standard residue type,position,sequence: w 276 1
read_al_374_> Non-standard residue type,position,sequence: w 277 1
read_al_374_> Non-standard residue type,position,sequence: w 278 1
read_al_374_> Non-standard residue type,position,sequence: w 279 1
read_al_374_> Non-standard residue type,position,sequence: w 280 1
read_al_374_> Non-standard residue type,position,sequence: w 281 1
read_al_374_> Non-standard residue type,position,sequence: w 282 1
read_al_374_> Non-standard residue type,position,sequence: w 283 1
read_al_374_> Non-standard residue type,position,sequence: w 284 1
read_al_374_> Non-standard residue type,position,sequence: w 285 1
read_al_374_> Non-standard residue type,position,sequence: w 286 1
read_al_374_> Non-standard residue type,position,sequence: w 287 1
read_al_374_> Non-standard residue type,position,sequence: w 288 1
read_al_374_> Non-standard residue type,position,sequence: w 289 1
read_al_374_> Non-standard residue type,position,sequence: w 290 1
read_al_374_> Non-standard residue type,position,sequence: w 291 1
read_al_374_> Non-standard residue type,position,sequence: w 292 1
read_al_374_> Non-standard residue type,position,sequence: w 293 1
read_al_374_> Non-standard residue type,position,sequence: w 294 1
read_al_374_> Non-standard residue type,position,sequence: w 295 1
read_al_374_> Non-standard residue type,position,sequence: w 296 1
read_al_374_> Non-standard residue type,position,sequence: w 297 1
read_al_374_> Non-standard residue type,position,sequence: w 298 1
read_al_374_> Non-standard residue type,position,sequence: w 299 1
read_al_374_> Non-standard residue type,position,sequence: w 300 1
read_al_374_> Non-standard residue type,position,sequence: w 301 1
read_al_374_> Non-standard residue type,position,sequence: w 302 1
read_al_374_> Non-standard residue type,position,sequence: w 303 1
read_al_374_> Non-standard residue type,position,sequence: w 304 1
read_al_374_> Non-standard residue type,position,sequence: w 305 1
read_al_374_> Non-standard residue type,position,sequence: w 306 1
read_al_374_> Non-standard residue type,position,sequence: w 307 1
read_al_374_> Non-standard residue type,position,sequence: w 308 1
read_al_374_> Non-standard residue type,position,sequence: w 309 1
read_al_374_> Non-standard residue type,position,sequence: w 310 1
read_al_374_> Non-standard residue type,position,sequence: w 311 1
read_al_374_> Non-standard residue type,position,sequence: w 312 1
read_al_374_> Non-standard residue type,position,sequence: w 313 1
read_al_374_> Non-standard residue type,position,sequence: w 314 1
read_al_374_> Non-standard residue type,position,sequence: w 315 1
read_al_374_> Non-standard residue type,position,sequence: w 316 1
read_al_374_> Non-standard residue type,position,sequence: w 317 1
read_al_374_> Non-standard residue type,position,sequence: w 318 1
read_al_374_> Non-standard residue type,position,sequence: w 319 1
read_al_374_> Non-standard residue type,position,sequence: w 320 1
read_al_374_> Non-standard residue type,position,sequence: w 321 1
read_al_374_> Non-standard residue type,position,sequence: w 322 1
read_al_374_> Non-standard residue type,position,sequence: w 323 1
read_al_374_> Non-standard residue type,position,sequence: w 324 1
read_al_374_> Non-standard residue type,position,sequence: w 325 1
read_al_374_> Non-standard residue type,position,sequence: w 326 1
read_al_374_> Non-standard residue type,position,sequence: w 327 1
read_al_374_> Non-standard residue type,position,sequence: w 328 1
read_al_374_> Non-standard residue type,position,sequence: w 329 1
read_al_374_> Non-standard residue type,position,sequence: w 330 1
read_al_374_> Non-standard residue type,position,sequence: w 331 1
read_al_374_> Non-standard residue type,position,sequence: w 332 1
read_al_374_> Non-standard residue type,position,sequence: w 333 1
read_al_374_> Non-standard residue type,position,sequence: w 334 1
read_al_374_> Non-standard residue type,position,sequence: w 335 1
read_al_374_> Non-standard residue type,position,sequence: w 336 1
read_al_374_> Non-standard residue type,position,sequence: w 337 1
read_al_374_> Non-standard residue type,position,sequence: w 338 1
read_al_374_> Non-standard residue type,position,sequence: w 339 1
read_al_374_> Non-standard residue type,position,sequence: w 340 1
read_al_374_> Non-standard residue type,position,sequence: w 341 1
read_al_374_> Non-standard residue type,position,sequence: w 342 1
read_al_374_> Non-standard residue type,position,sequence: w 343 1
read_al_374_> Non-standard residue type,position,sequence: w 344 1
read_al_374_> Non-standard residue type,position,sequence: w 345 1
read_al_374_> Non-standard residue type,position,sequence: w 346 1
read_al_374_> Non-standard residue type,position,sequence: w 347 1
read_al_374_> Non-standard residue type,position,sequence: w 348 1
read_al_374_> Non-standard residue type,position,sequence: w 349 1
read_al_374_> Non-standard residue type,position,sequence: w 350 1
read_al_374_> Non-standard residue type,position,sequence: w 351 1
read_al_374_> Non-standard residue type,position,sequence: w 352 1
read_al_374_> Non-standard residue type,position,sequence: w 353 1
read_al_374_> Non-standard residue type,position,sequence: w 354 1
read_al_374_> Non-standard residue type,position,sequence: w 355 1
read_al_374_> Non-standard residue type,position,sequence: w 356 1
read_al_374_> Non-standard residue type,position,sequence: w 357 1
read_al_374_> Non-standard residue type,position,sequence: w 358 1
read_al_374_> Non-standard residue type,position,sequence: w 359 1
read_al_374_> Non-standard residue type,position,sequence: w 360 1
read_al_374_> Non-standard residue type,position,sequence: w 361 1
read_al_374_> Non-standard residue type,position,sequence: w 362 1
read_al_374_> Non-standard residue type,position,sequence: w 363 1
read_al_374_> Non-standard residue type,position,sequence: w 364 1
read_al_374_> Non-standard residue type,position,sequence: w 365 1
read_al_374_> Non-standard residue type,position,sequence: w 366 1
read_al_374_> Non-standard residue type,position,sequence: w 367 1
read_al_374_> Non-standard residue type,position,sequence: w 368 1
read_al_374_> Non-standard residue type,position,sequence: w 123 2
read_al_374_> Non-standard residue type,position,sequence: w 124 2
read_al_374_> Non-standard residue type,position,sequence: w 125 2
read_al_374_> Non-standard residue type,position,sequence: w 126 2
read_al_374_> Non-standard residue type,position,sequence: w 127 2
read_al_374_> Non-standard residue type,position,sequence: w 128 2
read_al_374_> Non-standard residue type,position,sequence: w 129 2
read_al_374_> Non-standard residue type,position,sequence: w 130 2
read_al_374_> Non-standard residue type,position,sequence: w 131 2
read_al_374_> Non-standard residue type,position,sequence: w 132 2
read_al_374_> Non-standard residue type,position,sequence: w 133 2
read_al_374_> Non-standard residue type,position,sequence: w 134 2
read_al_374_> Non-standard residue type,position,sequence: w 135 2
read_al_374_> Non-standard residue type,position,sequence: w 136 2
read_al_374_> Non-standard residue type,position,sequence: w 137 2
read_al_374_> Non-standard residue type,position,sequence: w 138 2
read_al_374_> Non-standard residue type,position,sequence: w 139 2
read_al_374_> Non-standard residue type,position,sequence: w 140 2
read_al_374_> Non-standard residue type,position,sequence: w 141 2
read_al_374_> Non-standard residue type,position,sequence: w 142 2
read_al_374_> Non-standard residue type,position,sequence: w 143 2
read_al_374_> Non-standard residue type,position,sequence: w 144 2
read_al_374_> Non-standard residue type,position,sequence: w 145 2
read_al_374_> Non-standard residue type,position,sequence: w 146 2
read_al_374_> Non-standard residue type,position,sequence: w 147 2
read_al_374_> Non-standard residue type,position,sequence: w 148 2
read_al_374_> Non-standard residue type,position,sequence: w 149 2
read_al_374_> Non-standard residue type,position,sequence: w 150 2
read_al_374_> Non-standard residue type,position,sequence: w 151 2
read_al_374_> Non-standard residue type,position,sequence: w 152 2
read_al_374_> Non-standard residue type,position,sequence: w 153 2
read_al_374_> Non-standard residue type,position,sequence: w 154 2
read_al_374_> Non-standard residue type,position,sequence: w 155 2
read_al_374_> Non-standard residue type,position,sequence: w 156 2
read_al_374_> Non-standard residue type,position,sequence: w 157 2
read_al_374_> Non-standard residue type,position,sequence: w 158 2
read_al_374_> Non-standard residue type,position,sequence: w 159 2
read_al_374_> Non-standard residue type,position,sequence: w 160 2
read_al_374_> Non-standard residue type,position,sequence: w 161 2
read_al_374_> Non-standard residue type,position,sequence: w 162 2
read_al_374_> Non-standard residue type,position,sequence: w 163 2
read_al_374_> Non-standard residue type,position,sequence: w 164 2
read_al_374_> Non-standard residue type,position,sequence: w 165 2
read_al_374_> Non-standard residue type,position,sequence: w 166 2
read_al_374_> Non-standard residue type,position,sequence: w 167 2
read_al_374_> Non-standard residue type,position,sequence: w 168 2
read_al_374_> Non-standard residue type,position,sequence: w 169 2
read_al_374_> Non-standard residue type,position,sequence: w 170 2
read_al_374_> Non-standard residue type,position,sequence: w 171 2
read_al_374_> Non-standard residue type,position,sequence: w 172 2
read_al_374_> Non-standard residue type,position,sequence: w 173 2
read_al_374_> Non-standard residue type,position,sequence: w 174 2
read_al_374_> Non-standard residue type,position,sequence: w 175 2
read_al_374_> Non-standard residue type,position,sequence: w 176 2
read_al_374_> Non-standard residue type,position,sequence: w 177 2
read_al_374_> Non-standard residue type,position,sequence: w 178 2
read_al_374_> Non-standard residue type,position,sequence: w 179 2
read_al_374_> Non-standard residue type,position,sequence: w 180 2
read_al_374_> Non-standard residue type,position,sequence: w 181 2
read_al_374_> Non-standard residue type,position,sequence: w 182 2
read_al_374_> Non-standard residue type,position,sequence: w 183 2
read_al_374_> Non-standard residue type,position,sequence: w 184 2
read_al_374_> Non-standard residue type,position,sequence: w 185 2
read_al_374_> Non-standard residue type,position,sequence: w 186 2
read_al_374_> Non-standard residue type,position,sequence: w 187 2
read_al_374_> Non-standard residue type,position,sequence: w 188 2
read_al_374_> Non-standard residue type,position,sequence: w 189 2
read_al_374_> Non-standard residue type,position,sequence: w 190 2
read_al_374_> Non-standard residue type,position,sequence: w 191 2
read_al_374_> Non-standard residue type,position,sequence: w 192 2
read_al_374_> Non-standard residue type,position,sequence: w 193 2
read_al_374_> Non-standard residue type,position,sequence: w 194 2
read_al_374_> Non-standard residue type,position,sequence: w 195 2
read_al_374_> Non-standard residue type,position,sequence: w 196 2
read_al_374_> Non-standard residue type,position,sequence: w 197 2
read_al_374_> Non-standard residue type,position,sequence: w 198 2
read_al_374_> Non-standard residue type,position,sequence: w 199 2
read_al_374_> Non-standard residue type,position,sequence: w 200 2
read_al_374_> Non-standard residue type,position,sequence: w 201 2
read_al_374_> Non-standard residue type,position,sequence: w 202 2
read_al_374_> Non-standard residue type,position,sequence: w 203 2
read_al_374_> Non-standard residue type,position,sequence: w 204 2
read_al_374_> Non-standard residue type,position,sequence: w 205 2
read_al_374_> Non-standard residue type,position,sequence: w 206 2
read_al_374_> Non-standard residue type,position,sequence: w 207 2
read_al_374_> Non-standard residue type,position,sequence: w 208 2
read_al_374_> Non-standard residue type,position,sequence: w 209 2
read_al_374_> Non-standard residue type,position,sequence: w 210 2
read_al_374_> Non-standard residue type,position,sequence: w 211 2
read_al_374_> Non-standard residue type,position,sequence: w 212 2
read_al_374_> Non-standard residue type,position,sequence: w 213 2
read_al_374_> Non-standard residue type,position,sequence: w 214 2
read_al_374_> Non-standard residue type,position,sequence: w 215 2
read_al_374_> Non-standard residue type,position,sequence: w 216 2
read_al_374_> Non-standard residue type,position,sequence: w 217 2
read_al_374_> Non-standard residue type,position,sequence: w 218 2
read_al_374_> Non-standard residue type,position,sequence: w 219 2
read_al_374_> Non-standard residue type,position,sequence: w 220 2
read_al_374_> Non-standard residue type,position,sequence: w 221 2
read_al_374_> Non-standard residue type,position,sequence: w 222 2
read_al_374_> Non-standard residue type,position,sequence: w 223 2
read_al_374_> Non-standard residue type,position,sequence: w 224 2
read_al_374_> Non-standard residue type,position,sequence: w 225 2
read_al_374_> Non-standard residue type,position,sequence: w 226 2
read_al_374_> Non-standard residue type,position,sequence: w 227 2
read_al_374_> Non-standard residue type,position,sequence: w 228 2
read_al_374_> Non-standard residue type,position,sequence: w 229 2
read_al_374_> Non-standard residue type,position,sequence: w 230 2
read_al_374_> Non-standard residue type,position,sequence: w 231 2
read_al_374_> Non-standard residue type,position,sequence: w 232 2
read_al_374_> Non-standard residue type,position,sequence: w 233 2
read_al_374_> Non-standard residue type,position,sequence: w 234 2
read_al_374_> Non-standard residue type,position,sequence: w 235 2
read_al_374_> Non-standard residue type,position,sequence: w 236 2
read_al_374_> Non-standard residue type,position,sequence: w 237 2
read_al_374_> Non-standard residue type,position,sequence: w 238 2
read_al_374_> Non-standard residue type,position,sequence: w 239 2
read_al_374_> Non-standard residue type,position,sequence: w 240 2
read_al_374_> Non-standard residue type,position,sequence: w 241 2
read_al_374_> Non-standard residue type,position,sequence: w 242 2
read_al_374_> Non-standard residue type,position,sequence: w 243 2
read_al_374_> Non-standard residue type,position,sequence: w 244 2
read_al_374_> Non-standard residue type,position,sequence: w 245 2
read_al_374_> Non-standard residue type,position,sequence: w 246 2
read_al_374_> Non-standard residue type,position,sequence: w 247 2
read_al_374_> Non-standard residue type,position,sequence: w 248 2
read_al_374_> Non-standard residue type,position,sequence: w 249 2
read_al_374_> Non-standard residue type,position,sequence: w 250 2
read_al_374_> Non-standard residue type,position,sequence: w 251 2
read_al_374_> Non-standard residue type,position,sequence: w 252 2
read_al_374_> Non-standard residue type,position,sequence: w 253 2
read_al_374_> Non-standard residue type,position,sequence: w 254 2
read_al_374_> Non-standard residue type,position,sequence: w 255 2
read_al_374_> Non-standard residue type,position,sequence: w 256 2
read_al_374_> Non-standard residue type,position,sequence: w 257 2
read_al_374_> Non-standard residue type,position,sequence: w 258 2
read_al_374_> Non-standard residue type,position,sequence: w 259 2
read_al_374_> Non-standard residue type,position,sequence: w 260 2
read_al_374_> Non-standard residue type,position,sequence: w 261 2
read_al_374_> Non-standard residue type,position,sequence: w 262 2
read_al_374_> Non-standard residue type,position,sequence: w 263 2
read_al_374_> Non-standard residue type,position,sequence: w 264 2
read_al_374_> Non-standard residue type,position,sequence: w 265 2
read_al_374_> Non-standard residue type,position,sequence: w 266 2
read_al_374_> Non-standard residue type,position,sequence: w 267 2
read_al_374_> Non-standard residue type,position,sequence: w 268 2
read_al_374_> Non-standard residue type,position,sequence: w 269 2
read_al_374_> Non-standard residue type,position,sequence: w 270 2
read_al_374_> Non-standard residue type,position,sequence: w 271 2
read_al_374_> Non-standard residue type,position,sequence: w 272 2
read_al_374_> Non-standard residue type,position,sequence: w 273 2
read_al_374_> Non-standard residue type,position,sequence: w 274 2
read_al_374_> Non-standard residue type,position,sequence: w 275 2
read_al_374_> Non-standard residue type,position,sequence: w 276 2
read_al_374_> Non-standard residue type,position,sequence: w 277 2
read_al_374_> Non-standard residue type,position,sequence: w 278 2
read_al_374_> Non-standard residue type,position,sequence: w 279 2
read_al_374_> Non-standard residue type,position,sequence: w 280 2
read_al_374_> Non-standard residue type,position,sequence: w 281 2
read_al_374_> Non-standard residue type,position,sequence: w 282 2
read_al_374_> Non-standard residue type,position,sequence: w 283 2
read_al_374_> Non-standard residue type,position,sequence: w 284 2
read_al_374_> Non-standard residue type,position,sequence: w 285 2
read_al_374_> Non-standard residue type,position,sequence: w 286 2
read_al_374_> Non-standard residue type,position,sequence: w 287 2
read_al_374_> Non-standard residue type,position,sequence: w 288 2
read_al_374_> Non-standard residue type,position,sequence: w 289 2
read_al_374_> Non-standard residue type,position,sequence: w 290 2
read_al_374_> Non-standard residue type,position,sequence: w 291 2
read_al_374_> Non-standard residue type,position,sequence: w 292 2
read_al_374_> Non-standard residue type,position,sequence: w 293 2
read_al_374_> Non-standard residue type,position,sequence: w 294 2
read_al_374_> Non-standard residue type,position,sequence: w 295 2
read_al_374_> Non-standard residue type,position,sequence: w 296 2
read_al_374_> Non-standard residue type,position,sequence: w 297 2
read_al_374_> Non-standard residue type,position,sequence: w 298 2
read_al_374_> Non-standard residue type,position,sequence: w 299 2
read_al_374_> Non-standard residue type,position,sequence: w 300 2
read_al_374_> Non-standard residue type,position,sequence: w 301 2
read_al_374_> Non-standard residue type,position,sequence: w 302 2
read_al_374_> Non-standard residue type,position,sequence: w 303 2
read_al_374_> Non-standard residue type,position,sequence: w 304 2
read_al_374_> Non-standard residue type,position,sequence: w 305 2
read_al_374_> Non-standard residue type,position,sequence: w 306 2
read_al_374_> Non-standard residue type,position,sequence: w 307 2
read_al_374_> Non-standard residue type,position,sequence: w 308 2
read_al_374_> Non-standard residue type,position,sequence: w 309 2
read_al_374_> Non-standard residue type,position,sequence: w 310 2
read_al_374_> Non-standard residue type,position,sequence: w 311 2
read_al_374_> Non-standard residue type,position,sequence: w 312 2
read_al_374_> Non-standard residue type,position,sequence: w 313 2
read_al_374_> Non-standard residue type,position,sequence: w 314 2
read_al_374_> Non-standard residue type,position,sequence: w 315 2
read_al_374_> Non-standard residue type,position,sequence: w 316 2
read_al_374_> Non-standard residue type,position,sequence: w 317 2
read_al_374_> Non-standard residue type,position,sequence: w 318 2
read_al_374_> Non-standard residue type,position,sequence: w 319 2
read_al_374_> Non-standard residue type,position,sequence: w 320 2
read_al_374_> Non-standard residue type,position,sequence: w 321 2
read_al_374_> Non-standard residue type,position,sequence: w 322 2
read_al_374_> Non-standard residue type,position,sequence: w 323 2
read_al_374_> Non-standard residue type,position,sequence: w 324 2
read_al_374_> Non-standard residue type,position,sequence: w 325 2
read_al_374_> Non-standard residue type,position,sequence: w 326 2
read_al_374_> Non-standard residue type,position,sequence: w 327 2
read_al_374_> Non-standard residue type,position,sequence: w 328 2
read_al_374_> Non-standard residue type,position,sequence: w 329 2
read_al_374_> Non-standard residue type,position,sequence: w 330 2
read_al_374_> Non-standard residue type,position,sequence: w 331 2
read_al_374_> Non-standard residue type,position,sequence: w 332 2
read_al_374_> Non-standard residue type,position,sequence: w 333 2
read_al_374_> Non-standard residue type,position,sequence: w 334 2
read_al_374_> Non-standard residue type,position,sequence: w 335 2
read_al_374_> Non-standard residue type,position,sequence: w 336 2
read_al_374_> Non-standard residue type,position,sequence: w 337 2
read_al_374_> Non-standard residue type,position,sequence: w 338 2
read_al_374_> Non-standard residue type,position,sequence: w 339 2
read_al_374_> Non-standard residue type,position,sequence: w 340 2
read_al_374_> Non-standard residue type,position,sequence: w 341 2
read_al_374_> Non-standard residue type,position,sequence: w 342 2
read_al_374_> Non-standard residue type,position,sequence: w 343 2
read_al_374_> Non-standard residue type,position,sequence: w 344 2
read_al_374_> Non-standard residue type,position,sequence: w 345 2
read_al_374_> Non-standard residue type,position,sequence: w 346 2
read_al_374_> Non-standard residue type,position,sequence: w 347 2
read_al_374_> Non-standard residue type,position,sequence: w 348 2
read_al_374_> Non-standard residue type,position,sequence: w 349 2
read_al_374_> Non-standard residue type,position,sequence: w 350 2
read_al_374_> Non-standard residue type,position,sequence: w 351 2
read_al_374_> Non-standard residue type,position,sequence: w 352 2
read_al_374_> Non-standard residue type,position,sequence: w 353 2
read_al_374_> Non-standard residue type,position,sequence: w 354 2
read_al_374_> Non-standard residue type,position,sequence: w 355 2
read_al_374_> Non-standard residue type,position,sequence: w 356 2
read_al_374_> Non-standard residue type,position,sequence: w 357 2
read_al_374_> Non-standard residue type,position,sequence: w 358 2
read_al_374_> Non-standard residue type,position,sequence: w 359 2
read_al_374_> Non-standard residue type,position,sequence: w 360 2
read_al_374_> Non-standard residue type,position,sequence: w 361 2
read_al_374_> Non-standard residue type,position,sequence: w 362 2
read_al_374_> Non-standard residue type,position,sequence: w 363 2
read_al_374_> Non-standard residue type,position,sequence: w 364 2
read_al_374_> Non-standard residue type,position,sequence: w 365 2
read_al_374_> Non-standard residue type,position,sequence: w 366 2
read_al_374_> Non-standard residue type,position,sequence: w 367 2
read_al_374_> Non-standard residue type,position,sequence: w 368 2
Read the alignment from file : alignment.ali
Total number of alignment positions: 368
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 h-CLEC2.c 368 1 h-CLEC2.cif
2 chain_A 368 1 chain_A
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./h-CLEC2.cif_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520570 508.369
0.496
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520570 508.369 0.496
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 520741 508.536
0.497
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521591 509.366
0.497
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 522849 510.595
0.499
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 524753 512.454
0.500
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 527609 515.243
0.503
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 527609 515.243 0.503
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 527699 515.331
0.503
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 531983 519.515
0.507
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 531983 519.515 0.507
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 532118 519.646
0.507
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 538544 525.922
0.514
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 538544 525.922 0.514
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 538742 526.115
0.514
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 548364 535.512
0.523
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 548364 535.512 0.523
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 548661 535.802
0.523
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 548661 535.802 0.523
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 549111 536.241
0.524
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 563561 550.353
0.537
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 563561 550.353 0.537
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 564236 551.012
0.538
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 564236 551.012 0.538
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 565244 551.996
0.539
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 565244 551.996 0.539
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 566756 553.473
0.541
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 565523 552.269
0.539
fndatmi_285W> Only 122 residues out of 368 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 122 residues out of 368 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
\----------------------------------------------
END OF TABLE
check_a_344_> Open ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file: 3
openf___224_> Open ${LIB}/par.lib
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 704775 688.257
0.672
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 706375 689.819
0.674
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 710355 693.706
0.677
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 712355 695.659
0.679
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 715355 698.589
0.682
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 719855 702.983
0.687
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 725427 708.425
0.692
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 728227 711.159
0.694
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 732427 715.261
0.698
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 738727 721.413
0.705
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 741499 724.120
0.707
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 742899 725.487
0.708
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 800518 781.756 0.763
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 926644 904.926 0.884
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 942492 920.402 0.899
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 122
atom names : C +N
atom indices : 1021 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 6 122
atom names : C CA +N O
atom indices : 1021 1020 0 1022
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 368 1268 1051 0 0 465
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 986292 963.176 0.941
patch_______> segment topology patched using RTF: 1 ; SER ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 368 1268 1051 1415 1678 465
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1030772 1006.613 0.983
patch_______> segment topology patched using RTF: 122 ; GLY ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 368 1269 1052 1417 1679 466
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 368 1269 1052 1417 1679 466
fndatmi_285W> Only 122 residues out of 368 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1041208 1016.805 0.993
patch_______> segment topology patched using RTF: 3 14 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 368 1269 1053 1419 1682 466
patch_______> segment topology patched using RTF: 31 117 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 368 1269 1054 1421 1685 466
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1041456 1017.047 0.993
patch_______> segment topology patched using RTF: 96 109 ; CYS CYS ; DISU
segments residues atoms bonds angles dihedrals impropers:
1 368 1269 1055 1423 1688 466
patch_s_522_> Number of disulfides patched in MODEL: 3
transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer: 1
After transferring coordinates of the equivalent template atoms,
there are defined, undefined atoms in MODEL: 1267 2
openf___224_> Open chain_A.ini
wrpdb___568_> Residues, atoms, selected atoms: 368 1269 1269
make_re_417_> Restraint type to be calculated: stereo
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1148905 1121.978
1.096
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1157097 1129.978
1.103
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1173481 1145.978
1.119
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1206249 1177.978
1.150
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1239017 1209.978
1.182
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1304553 1273.978
1.244
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1337321 1305.978
1.275
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1370089 1337.978
1.307
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1435625 1401.978
1.369
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 1055 1423 1597 464
Total number of restraints before, now : 0 4539
make_re_422_> Number of previous, current restraints : 0 4539
make_re_423_> Number of previous, current selected restraints: 0 4539
make_re_417_> Restraint type to be calculated: phi-psi_binormal
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1591518 1554.217
1.518
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.mdt
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 121
ALA
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 122
GLY
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 3 122
GLY
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 122
GLY
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 1
SER
getdata_643_> Protein accepted: h-CLEC2.cif_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1722606 1682.232
1.643
make_re_422_> Number of previous, current restraints : 4539 4659
make_re_423_> Number of previous, current selected restraints: 4539 4659
make_re_417_> Restraint type to be calculated: omega_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1722606 1682.232
1.643
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/omega.mdt
getdata_643_> Protein accepted: h-CLEC2.cif_1
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 123
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 4659 4780
make_re_423_> Number of previous, current selected restraints: 4659 4657
make_re_417_> Restraint type to be calculated: chi1_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1722606 1682.232
1.643
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1.mdt
getdata_643_> Protein accepted: h-CLEC2.cif_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1788142 1746.232
1.705
make_re_422_> Number of previous, current restraints : 4780 4890
make_re_423_> Number of previous, current selected restraints: 4657 4767
make_re_417_> Restraint type to be calculated: chi2_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1788142 1746.232
1.705
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi2.mdt
getdata_643_> Protein accepted: h-CLEC2.cif_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1853678 1810.232
1.768
make_re_422_> Number of previous, current restraints : 4890 4977
make_re_423_> Number of previous, current selected restraints: 4767 4854
make_re_417_> Restraint type to be calculated: chi3_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1853678 1810.232
1.768
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi3.mdt
getdata_643_> Protein accepted: h-CLEC2.cif_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 4977 5012
make_re_423_> Number of previous, current selected restraints: 4854 4889
make_re_417_> Restraint type to be calculated: chi4_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1853678 1810.232
1.768
openf___224_> Open ${MODINSTALL10v6}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v6}/modlib/chi4.mdt
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted: h-CLEC2.cif_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 5012 5028
make_re_423_> Number of previous, current selected restraints: 4889 4905
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2219114 2167.104
2.116
make_re_422_> Number of previous, current restraints : 5028 7290
make_re_423_> Number of previous, current selected restraints: 4905 7167
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2350186 2295.104
2.241
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2612330 2551.104
2.491
make_re_422_> Number of previous, current restraints : 7290 9702
make_re_423_> Number of previous, current selected restraints: 7167 9579
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2743402 2679.104
2.616
make_re_422_> Number of previous, current restraints : 9702 11874
make_re_423_> Number of previous, current selected restraints: 9579 11751
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2874474 2807.104
2.741
make_re_422_> Number of previous, current restraints : 11874 13337
make_re_423_> Number of previous, current selected restraints: 11751 13214
246 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 13337 13338
make_re_423_> Number of previous, current selected restraints: 13214 13215
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 13338 15856
make_re_423_> Number of previous, current selected restraints: 13215 15733
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 15856 15856
make_re_423_> Number of previous, current selected restraints: 15733 15733
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3136618 3063.104
2.991
make_re_422_> Number of previous, current restraints : 15856 16871
make_re_423_> Number of previous, current selected restraints: 15733 16748
0 atoms in residues without defined topology
constrained to be rigid bodies
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 16871 16871
make_re_423_> Number of previous, current selected restraints: 16748 16748
rmdupl__427_> 749 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 16871 15999
openf___224_> Open chain_A.rsr
openf___224_> Open chain_A.rsr
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2940098 2871.189
2.804
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3333314 3255.189
3.179
rdcsr2__307_> Number of restraints read : 15999
Number of excluded pairs read: 1
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 15999 15999
Explicitly excluded atom pairs in memory : 1
Pseudo atoms in memory : 0
No output models from Modeller; see log for Modeller text output.
> ui windowfill toggle
> select add #1
1267 atoms, 1053 bonds, 30 pseudobonds, 368 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> select /A:106-109,112-121,136-137,157-162,195-199,202-206,212-219
359 atoms, 369 bonds, 40 residues, 1 model selected
> open /Users/wendyk/Downloads/2EAK.cif
Summary of feedback from opening /Users/wendyk/Downloads/2EAK.cif
---
notes | Fetching CCD DTV from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/DTV/DTV.cif
Fetching CCD GAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GAL/GAL.cif
Fetching CCD GLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/GLC/GLC.cif
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif
2EAK.cif title:
Crystal structure of human galectin-9 N-terminal CRD in complex with lactose
[more info...]
Chain information for 2EAK.cif #2
---
Chain | Description | UniProt
A B C | Galectin-9 | LEG9_HUMAN 1-148
Non-standard residues in 2EAK.cif #2
---
DTV — (2S,3S)-1,4-dimercaptobutane-2,3-diol
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
GOL — glycerol (glycerin; propane-1,2,3-triol)
2EAK.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> sym #2 assembly 1
Made 1 copies for 2EAK.cif assembly 1
> view
> select add #1
1267 atoms, 1053 bonds, 30 pseudobonds, 368 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select subtract #1
Nothing selected
> select add #3
1273 atoms, 1184 bonds, 267 residues, 2 models selected
> show sel atoms
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> nucleotides sel stubs
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> color sel byhetero
> open /Users/wendyk/Downloads/pdb2eak.ent
pdb2eak.ent title:
Crystal structure of human galectin-9 N-terminal CRD In complex with lactose
[more info...]
Chain information for pdb2eak.ent #4
---
Chain | Description | UniProt
A B C | galectin-9 | LEG9_HUMAN 1-148
Non-standard residues in pdb2eak.ent #4
---
DTV — (2S,3S)-1,4-dimercaptobutane-2,3-diol
GAL — β-D-galactopyranose (β-D-galactose; D-galactose; galactose)
GLC — α-D-glucopyranose (α-D-glucose; D-glucose; glucose)
GOL — glycerol (glycerin; propane-1,2,3-triol)
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #4 models
> hide #3.1 models
> show #3.1 models
> open /Users/wendyk/Downloads/GRAMMresults-120285/ligand_model1.pdb
Summary of feedback from opening
/Users/wendyk/Downloads/GRAMMresults-120285/ligand_model1.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK Docking models Generated by GRAMM
Chain information for ligand_model1.pdb #5
---
Chain | Description
E | No description available
Computing secondary structure
> hide #5 models
> open /Users/wendyk/Downloads/GRAMMresults-120285/receptor-ligand_model1.pdb
Summary of feedback from opening
/Users/wendyk/Downloads/GRAMMresults-120285/receptor-ligand_model1.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK Docking models Generated by GRAMM
Chain information for receptor-ligand_model1.pdb #6
---
Chain | Description
A | No description available
B C | No description available
E | No description available
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> hide #1.1 models
> hide #!1 models
> hide #3.1 models
> hide #!3 models
> select subtract #3
Nothing selected
> select add #3.1
1273 atoms, 1184 bonds, 267 residues, 1 model selected
> hide #6 models
> show #6 models
> style #6 stick
Changed 4691 atom styles
> style #6 stick
Changed 4691 atom styles
> show #6 atoms
> hide #6 atoms
> show #6 cartoons
> hide #6 cartoons
> show #6 cartoons
> style #6 sphere
Changed 4691 atom styles
> style #6 sphere
Changed 4691 atom styles
> style #6 sphere
Changed 4691 atom styles
> style #6 sphere
Changed 4691 atom styles
> style #6 stick
Changed 4691 atom styles
> select down
1273 atoms, 1184 bonds, 267 residues, 1 model selected
> select down
1273 atoms, 1184 bonds, 267 residues, 1 model selected
> select down
1273 atoms, 1184 bonds, 267 residues, 1 model selected
> open /Users/wendyk/Downloads/GRAMMresults-120285/receptor-ligand_model2.pdb
Summary of feedback from opening
/Users/wendyk/Downloads/GRAMMresults-120285/receptor-ligand_model2.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK Docking models Generated by GRAMM
Chain information for receptor-ligand_model2.pdb #7
---
Chain | Description
A | No description available
B C | No description available
E | No description available
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #7 models
> open /Users/wendyk/Downloads/GRAMMresults-120285/receptor-ligand_model3.pdb
Summary of feedback from opening
/Users/wendyk/Downloads/GRAMMresults-120285/receptor-ligand_model3.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK Docking models Generated by GRAMM
Chain information for receptor-ligand_model3.pdb #8
---
Chain | Description
A | No description available
B C | No description available
E | No description available
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> select add #8
5964 atoms, 5724 bonds, 1097 residues, 2 models selected
> select subtract #8
1273 atoms, 1184 bonds, 267 residues, 1 model selected
> select add #8
5964 atoms, 5724 bonds, 1097 residues, 2 models selected
> select #8/A:6-148
1121 atoms, 1153 bonds, 143 residues, 1 model selected
> select #8/B:7-148
1100 atoms, 1131 bonds, 142 residues, 1 model selected
> select #8/C:7-148
1114 atoms, 1146 bonds, 142 residues, 1 model selected
> select #8/E:100-221
1021 atoms, 1050 bonds, 122 residues, 1 model selected
> set bgColor white
> set bgColor #ffffff00
> rainbow sel
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
receptor-ligand_model3.pdb #8/E SER 100 CB
receptor-ligand_model3.pdb #8/E SER 100 OG
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for receptor-ligand_model3.pdb_E SES surface #8.1: minimum,
-13.49, mean -1.14, maximum 12.02
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for receptor-ligand_model3.pdb_E SES surface #8.1: minimum,
-13.49, mean -1.14, maximum 12.02
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for receptor-ligand_model3.pdb_E SES surface #8.1: minimum,
-13.49, mean -1.14, maximum 12.02
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor sel
1021 atoms, 122 residues, 1 surfaces, atom bfactor range 0 to 0
> color bfactor sel
1021 atoms, 122 residues, 1 surfaces, atom bfactor range 0 to 0
> mlp sel
Map values for surface "receptor-ligand_model3.pdb_E SES surface": minimum
-25.26, mean -5.826, maximum 21.62
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for receptor-ligand_model3.pdb_E SES surface #8.1: minimum,
-13.49, mean -1.14, maximum 12.02
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow sel
> style sel stick
Changed 1021 atom styles
> undo
> color sel bynucleotide
> color bfactor sel
1021 atoms, 122 residues, 1 surfaces, atom bfactor range 0 to 0
> style sel sphere
Changed 1021 atom styles
> style sel stick
Changed 1021 atom styles
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> color #8 #9dfa7dff
> color #8 #4dfa26ff
> color #8 #8fe1faff
> color #8.1 #f95e8dff
> select subtract #8.1
1 model selected
> hide #8.1 models
> show #8.1 models
> sequence chain #1/A#5/E#6/E#7/E#8/E
Alignment identifier is 1
> sequence chain #2/A,B,C#3.1/A#4/A,B,C
Alignment identifier is 2
> sequence chain #6/A#7/A#8/A
Alignment identifier is 3
> sequence chain #6/B,C#7/B,C#8/B,C
Alignment identifier is 4
> select add #8.1
1021 atoms, 122 residues, 1 model selected
> select add #7
5712 atoms, 4540 bonds, 952 residues, 3 models selected
> select subtract #7
1021 atoms, 122 residues, 2 models selected
> hide #8.1 models
> hide #!8 models
> select subtract #8.1
1 model selected
> select add #8
4691 atoms, 4540 bonds, 830 residues, 1 model selected
> select subtract #8
1 model selected
> show #!8 models
> hide #!8 models
> show #7 models
> select add #7
4691 atoms, 4540 bonds, 830 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #7 models
> show #6 models
> ui tool show Contacts
> select add #6
4691 atoms, 4540 bonds, 830 residues, 1 model selected
> color #6 #00fdffff
> color #6 #0096ffff
> view #7 clip false
> color /E indigo
> color /E pink
> color /E strawberry
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #6/E
1044 atoms, 1074 bonds, 124 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> color sel orange
> color sel orange red
> color sel cyan
> color sel cornflower blue
> color sel hot pink
> color sel magenta
> color sel hot pink
> color sel yellow
> color sel orange
> color sel orange red
> color sel red
> color sel purple
> color sel magenta
> color sel hot pink
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select add #6
4691 atoms, 4540 bonds, 830 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #6
4691 atoms, 4540 bonds, 830 residues, 1 model selected
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #6/B,C
Alignment identifier is 1
> sequence chain #6/E
Alignment identifier is 6/E
> select
> #6/B-C:17-20,30-37,45-50,58-65,71-75,86-88,98-105,109-114,117-123,133-138,140-148
1150 atoms, 1162 bonds, 140 residues, 1 model selected
> select #1/A:122-133,142-151,179-185
251 atoms, 254 bonds, 29 residues, 1 model selected
> interfaces #6 & ~solvent
3 buried areas: B E 1072, C E 1072, A B 385
Matplotlib is building the font cache; this may take a moment.
> label sel bgColor white color yellow
> label sel bgColor white color purple
> transparency ~sel 80 target c
> transparency ~sel 70 target c
> transparency ~sel 60 target c
> transparency ~sel 65 target c
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
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: Mac16,12
Model Number: MC6V4CH/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 24 GB
System Firmware Version: 13822.41.1
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.2 (24G325)
Kernel Version: Darwin 24.6.0
Time since boot: 9天3小时
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina 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: 4.12.0
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-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
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-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: 2.7.11
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: 7.13.0
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: 4.25.1
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: 3.2.5
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
pytz: 2025.2
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: 4.0.0
roman-numerals-py: 4.0.0
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
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: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
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
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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