Opened 14 months ago
Closed 14 months ago
#15914 closed defect (duplicate)
Crash on Mac waking from sleep
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Window Toolkit | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070002e1a7000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070002d1a4000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070002c1a1000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070002b19e000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070002a19b000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700029198000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700028195000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700027192000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070002618f000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070002518c000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700024189000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700023186000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700022183000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700021180000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070002017d000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070001f17a000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070001e177000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070001d174000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070001c171000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070001b16e000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x000070001a16b000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700019168000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Thread 0x0000700018165000 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap Current thread 0x00007ff85dd9ddc0 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.core._mac_util, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62) {"app_name":"ChimeraX","timestamp":"2024-09-09 13:16:02.00 -0500","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"2201444A-A859-44A8-95A1-363D5E26CD1A"} { "uptime" : 1100000, "procRole" : "Background", "version" : 2, "userID" : 502, "deployVersion" : 210, "modelCode" : "iMac20,1", "coalitionID" : 3129, "osVersion" : { "train" : "macOS 14.6.1", "build" : "23G93", "releaseType" : "User" }, "captureTime" : "2024-09-09 13:16:00.3185 -0500", "codeSigningMonitor" : 0, "incident" : "2201444A-A859-44A8-95A1-363D5E26CD1A", "pid" : 5252, "cpuType" : "X86-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2024-09-06 10:46:23.3582 -0500", "procStartAbsTime" : 910623989090428, "procExitAbsTime" : 1178791897092069, "procName" : "ChimeraX", "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX", "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"}, "storeInfo" : {"deviceIdentifierForVendor":"7DE7F1BA-7E0E-5EF3-8AF1-B22530389684","thirdParty":true}, "parentProc" : "tcsh", "parentPid" : 18570, "coalitionName" : "com.apple.Terminal", "crashReporterKey" : "D77CBDCE-560E-A76E-6409-11E87F8970FF", "responsiblePid" : 18493, "responsibleProc" : "Terminal", "codeSigningID" : "edu.ucsf.cgl.ChimeraX", "codeSigningTeamID" : "LWV8X224YF", "codeSigningFlags" : 570491649, "codeSigningValidationCategory" : 6, "codeSigningTrustLevel" : 4294967295, "bridgeVersion" : {"build":"21P6074","train":"8.6"}, "sip" : "enabled", "vmRegionInfo" : "0 is not in any region. 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"45f4e2a5-551b-4bc2-a2dc-19c244dda8f8", "experimentId" : "6643969b3099cf28e049862f", "deploymentId" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open alphafold_runs_0p_2p.cxs Log from Fri Aug 9 15:07:48 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open alphafold_runs_0p_2p.cxs Log from Thu Aug 8 17:23:41 2024 > alias dd distance delete > alias rd ui mousemode right distance > alias rs ui mousemode right select > alias nmr1 hide #1.2-20 models > alias slall label sel text > "{0.label_one_letter_code}{0.number}{0.insertion_code}" > alias lmearo label #1:thr,met,ala,leu,val,ile,phe,tyr text > "{0.label_one_letter_code}{0.number}{0.insertion_code}" > alias showbb show #1@N,C,CA,O,H; cartoon #1 suppress false; transparency #1 > 50 target c; hide #1:hoh > alias hidebb hide #1@N,C,CA,O,H target a; transparency $1 0 target c > alias sdist ui tool show Distances > alias showmet show #1:ile,leu,val,met,ala,thr target a; hide H; color #1:ile > paleturquoise target a; color #1:leu lightsalmon target a; color #1:val > khaki target a; color #1:met thistle target a; color #1:ala yellowgreen > target ab; color #1:thr aquamarine target a;color byhetero target a ; style > #1 ball > alias showmet2 show #2:ile,leu,val,met,ala,thr target a; hide H; color > #2:ile paleturquoise target a; color #2:leu lightsalmon target a; color > #2:val khaki target a; color #2:met thistle target a; color #2:ala > yellowgreen target ab; color #2:thr aquamarine target a;color byhetero > target a ; style #2 ball > alias showmet3 show #3:ile,leu,val,met,ala,thr target a; hide H; color > #3:ile paleturquoise target a; color #3:leu lightsalmon target a; color > #3:val khaki target a; color #3:met thistle target a; color #3:ala > yellowgreen target ab; color #3:thr aquamarine target a;color byhetero > target a ; style #3 ball > alias showaro show #1:phe,tyr,his,trp target ab; hide H; color #1:phe plum > target a; color #1:tyr lightpink target a; color byhetero target a > ui mousemode right distance > alias fgfr1_brake show #1: 546,562,638 > alias fgfr2_brake show #1: 549,565,641 > alias fgfr3_brake show #1: 540,556,632 > alias fgfr4_brake show #1: 535,551,627 UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open fold_kd_ctail_0p_run_1_model_0.cif Chain information for fold_kd_ctail_0p_run_1_model_0.cif #1 --- Chain | Description A | . > open > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_4.cif Chain information for fold_kd_ctail_0p_run_1_model_1.cif #2 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_1_model_2.cif #3 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_1_model_3.cif #4 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_1_model_4.cif #5 --- Chain | Description A | . > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_1.cif, chain A (#2), sequence alignment score = 1871 RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs: 4.590) > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_2.cif, chain A (#3), sequence alignment score = 1887.8 RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs: 21.274) > matchmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_3.cif, chain A (#4), sequence alignment score = 1881.8 RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs: 8.985) > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_4.cif, chain A (#5), sequence alignment score = 1871 RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs: 24.527) > open > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_4.cif Chain information for fold_kd_ctail_0p_run_2_model_0.cif #6 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_1.cif #7 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_2.cif #8 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_3.cif #9 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_4.cif #10 --- Chain | Description A | . > matchmaker #6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_0.cif, chain A (#6), sequence alignment score = 1887.8 RMSD between 365 pruned atom pairs is 0.000 angstroms; (across all 365 pairs: 0.000) > matchmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_1.cif, chain A (#7), sequence alignment score = 1871 RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs: 4.590) > matchmaker #8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_2.cif, chain A (#8), sequence alignment score = 1887.8 RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs: 21.274) > matchmaker #9 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_3.cif, chain A (#9), sequence alignment score = 1881.8 RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs: 8.985) > matchmaker #10 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_4.cif, chain A (#10), sequence alignment score = 1871 RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs: 24.527) > open /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_4.cif Chain information for fold_kd_ctail_2p_model_0.cif #11 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_1.cif #12 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_2.cif #13 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_3.cif #14 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_4.cif #15 --- Chain | Description A | . > matchmaker #1? to #1 Missing or invalid "matchAtoms" argument: only initial part "#1" of atom specifier valid > matchmaker #11 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_0.cif, chain A (#11), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.401 angstroms; (across all 365 pairs: 28.856) > matchmaker #12 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_1.cif, chain A (#12), sequence alignment score = 1833.8 RMSD between 273 pruned atom pairs is 0.368 angstroms; (across all 365 pairs: 31.133) > matchmaker #13 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_2.cif, chain A (#13), sequence alignment score = 1842.8 RMSD between 265 pruned atom pairs is 0.376 angstroms; (across all 365 pairs: 27.667) > matchmaker #14 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_3.cif, chain A (#14), sequence alignment score = 1842.8 RMSD between 271 pruned atom pairs is 0.446 angstroms; (across all 365 pairs: 28.883) > matchmaker #15 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_4.cif, chain A (#15), sequence alignment score = 1833.8 RMSD between 269 pruned atom pairs is 0.368 angstroms; (across all 365 pairs: 28.340) > matchmaker #16 to #1 No molecules/chains to match specified > open > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_4.cif Chain information for fold_kd_ctail_2p_run_2_model_0.cif #16 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_1.cif #17 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_2.cif #18 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_3.cif #19 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_4.cif #20 --- Chain | Description A | . > matchmaker #16 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_0.cif, chain A (#16), sequence alignment score = 1821.8 RMSD between 269 pruned atom pairs is 0.342 angstroms; (across all 365 pairs: 29.041) > matchmaker #17 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_1.cif, chain A (#17), sequence alignment score = 1821.8 RMSD between 270 pruned atom pairs is 0.304 angstroms; (across all 365 pairs: 34.580) > matchmaker #18 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_2.cif, chain A (#18), sequence alignment score = 1827.8 RMSD between 269 pruned atom pairs is 0.331 angstroms; (across all 365 pairs: 29.393) > matchmaker #19 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_3.cif, chain A (#19), sequence alignment score = 1863.8 RMSD between 278 pruned atom pairs is 0.415 angstroms; (across all 365 pairs: 13.710) > matchmaker #20 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_4.cif, chain A (#20), sequence alignment score = 1833.8 RMSD between 271 pruned atom pairs is 0.330 angstroms; (across all 365 pairs: 29.597) > ui tool show "Renumber Residues" > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458 7300 residues renumbered > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458 0 residues renumbered > show :771 > hide #1-10 target m > show #1-10 target m > hide #11-20 target m > show :653,654 > show #11-20 target m > hide #1-10 target m > show #1-10 target m > hide #1-10 target m > hide :780-822 > hide :780-822 cartoons > show #1-10 target m > show :695-725 atoms > show :767-779 atoms > hide #1-10 target m > show #1-10 target m > hide #1-10 target m > hide #11-19 target m > color #20:767-779 green target c > color #20:767-779 byelement target a > show :694 atoms > distance #20/A:694@CE1 #20/A:767@CD1 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU 767 CD1: 6.998Å > distance #20/A:694@CE1 #20/A:767@CD2 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU 767 CD2: 6.279Å > distance #20/A:696@CD1 #20/A:769@CD1 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU 769 CD1: 2.824Å > distance #20/A:696@CD1 #20/A:769@CD2 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU 769 CD2: 4.764Å > ~distance #20/A:696@CD1 #20/A:769@CD2 > distance #20/A:695@CG2 #20/A:773@CD2 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU 773 CD2: 5.040Å > ~distance #20/A:695@CG2 #20/A:773@CD2 > distance #20/A:695@CG2 #20/A:773@CD1 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU 773 CD1: 6.542Å > ~distance #20/A:695@CG2 #20/A:773@CD1 > hide :780-822 cartoons > hide :766-822 cartoons > distance #20/A:724@ND2 #20/A:768@O Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and ASP 768 O: 3.574Å > distance #20/A:724@ND2 #20/A:767@O Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and LEU 767 O: 5.063Å > hide :766-822 atoms > save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD- > Ctail/alphafold_runs_0p_2p.pdb > save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD- > Ctail/alphafold_runs_0p_2p.cxs ——— End of log from Thu Aug 8 17:23:41 2024 ——— opened ChimeraX session > open > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_4.cif Chain information for fold_kd_ctail_y653p_run_1_model_0.cif #22 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_1.cif #23 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_2.cif #24 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_3.cif #25 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_4.cif #26 --- Chain | Description A | . > matchmaker #22-26 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_0.cif, chain A (#22), sequence alignment score = 1869.8 RMSD between 281 pruned atom pairs is 0.444 angstroms; (across all 365 pairs: 16.950) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_1.cif, chain A (#23), sequence alignment score = 1827.8 RMSD between 269 pruned atom pairs is 0.326 angstroms; (across all 365 pairs: 25.654) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_2.cif, chain A (#24), sequence alignment score = 1833.8 RMSD between 268 pruned atom pairs is 0.334 angstroms; (across all 365 pairs: 27.277) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_3.cif, chain A (#25), sequence alignment score = 1827.8 RMSD between 269 pruned atom pairs is 0.345 angstroms; (across all 365 pairs: 28.333) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_4.cif, chain A (#26), sequence alignment score = 1830.8 RMSD between 270 pruned atom pairs is 0.353 angstroms; (across all 365 pairs: 27.133) > show #11-20 target m > hide :780-822 cartoons > open > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_4.cif Chain information for fold_kd_ctail_y653p_run_2_model_0.cif #27 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_1.cif #28 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_2.cif #29 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_3.cif #30 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_4.cif #31 --- Chain | Description A | . > matchmaker #27-31 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_0.cif, chain A (#27), sequence alignment score = 1827.8 RMSD between 268 pruned atom pairs is 0.409 angstroms; (across all 365 pairs: 31.267) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_1.cif, chain A (#28), sequence alignment score = 1842.8 RMSD between 273 pruned atom pairs is 0.458 angstroms; (across all 365 pairs: 31.317) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_2.cif, chain A (#29), sequence alignment score = 1833.8 RMSD between 268 pruned atom pairs is 0.382 angstroms; (across all 365 pairs: 29.220) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_3.cif, chain A (#30), sequence alignment score = 1836.8 RMSD between 266 pruned atom pairs is 0.366 angstroms; (across all 365 pairs: 28.088) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_4.cif, chain A (#31), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.691 angstroms; (across all 365 pairs: 30.898) > ui tool show "Renumber Residues" > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A > #26/A #27/A #28/A #29/A #30/A #31/A seqStart 458 3650 residues renumbered > hide :780-822 cartoons > show :766-780 cartoons > open > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_4.cif Chain information for fold_kd_ctail_y654p_run_1_model_0.cif #32 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_1.cif #33 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_2.cif #34 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_3.cif #35 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_4.cif #36 --- Chain | Description A | . > open > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_4.cif Chain information for fold_kd_ctail_y654p_run_2_model_0.cif #37 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_1.cif #38 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_2.cif #39 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_3.cif #40 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_4.cif #41 --- Chain | Description A | . > matchmaker #32-41 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_0.cif, chain A (#32), sequence alignment score = 1830.8 RMSD between 274 pruned atom pairs is 0.339 angstroms; (across all 365 pairs: 30.830) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_1.cif, chain A (#33), sequence alignment score = 1833.8 RMSD between 273 pruned atom pairs is 0.367 angstroms; (across all 365 pairs: 29.517) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_2.cif, chain A (#34), sequence alignment score = 1833.8 RMSD between 275 pruned atom pairs is 0.503 angstroms; (across all 365 pairs: 33.883) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_3.cif, chain A (#35), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.398 angstroms; (across all 365 pairs: 28.779) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_4.cif, chain A (#36), sequence alignment score = 1842.8 RMSD between 265 pruned atom pairs is 0.443 angstroms; (across all 365 pairs: 28.961) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_0.cif, chain A (#37), sequence alignment score = 1827.8 RMSD between 274 pruned atom pairs is 0.440 angstroms; (across all 365 pairs: 30.375) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_1.cif, chain A (#38), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.466 angstroms; (across all 365 pairs: 31.050) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_2.cif, chain A (#39), sequence alignment score = 1833.8 RMSD between 274 pruned atom pairs is 0.336 angstroms; (across all 365 pairs: 29.924) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_3.cif, chain A (#40), sequence alignment score = 1833.8 RMSD between 271 pruned atom pairs is 0.449 angstroms; (across all 365 pairs: 28.353) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_4.cif, chain A (#41), sequence alignment score = 1833.8 RMSD between 270 pruned atom pairs is 0.399 angstroms; (across all 365 pairs: 32.127) > hide :780-822 cartoons > ui tool show "Renumber Residues" > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A > #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A > #38/A #39/A #40/A #41/A seqStart 458 3650 residues renumbered > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A > #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A > #38/A #39/A #40/A #41/A seqStart 458 0 residues renumbered > hide :780-822 cartoons > hide cartoons > hide atoms > show :695-725 cartoons > show #1-10 target m > show :695-725 atoms > hide #1-10 target m > coulombic #41:720 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue PTR (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2 -fi mol2 -o /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2); atoms read (36), bonds read (36).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 166; net charge: -2` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface #41.1: minimum, -14.09, mean -2.42, maximum 12.27 > coulombic #41:695-725 Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface #41.1: minimum, -14.09, mean -2.42, maximum 12.27 > show :766-780 cartoons > hide #!41 models > show #!41 models > hide #!41 models > coulombic #40:766-780 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue PTR (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2 -fi mol2 -o /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2); atoms read (34), bonds read (34).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 164; net charge: -2` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Coulombic values for fold_kd_ctail_y654p_run_2_model_3.cif_A SES surface #40.1: minimum, -13.70, mean -2.40, maximum 12.19 > show #!41 models > coulombic #41:766-780 Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface #41.1: minimum, -14.09, mean -2.42, maximum 12.27 > hide #11-20,22-39#!40-41 surfaces > show :458-780 cartoons > show #1-10 target m > show :653,654 atoms > hide #1-10 target m > hide #11-20 target m > show #11-20 target m > hide #22-31 target m > hide #32-39#!40-41 target m > show #11-20 target m > show #22-39#!40 target m > hide #12 models > show #12 models > hide #11 models > show #11 models > hide #14 models > show #14 models > hide #16 models > show #16 models > hide #22 models > hide #19 models > hide #12-39#!40-41 target m > show #1-10 target m > hide #1-10 target m > save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD- > Ctail/alphafold_runs_0p_2p.cxs ——— End of log from Fri Aug 9 15:07:48 2024 ——— opened ChimeraX session > open > /Users/ksinha01/Kinases_local/FGFR1/FGFR1_struc_calc/fgfr1_03132024_v2/CNS/fgfr1_03132024_v2.pdb > format pdb Chain information for fgfr1_03132024_v2.pdb --- Chain | Description 42.1/A 42.2/A 42.3/A 42.4/A 42.5/A 42.6/A 42.7/A 42.8/A 42.9/A 42.10/A 42.11/A 42.12/A 42.13/A 42.14/A 42.15/A 42.16/A 42.17/A 42.18/A 42.19/A 42.20/A | No description available > matchmaker #42 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.1), sequence alignment score = 1439.2 RMSD between 151 pruned atom pairs is 1.266 angstroms; (across all 308 pairs: 6.495) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.2), sequence alignment score = 1419.4 RMSD between 124 pruned atom pairs is 1.241 angstroms; (across all 308 pairs: 6.760) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.3), sequence alignment score = 1427.8 RMSD between 115 pruned atom pairs is 1.181 angstroms; (across all 308 pairs: 6.912) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.4), sequence alignment score = 1450.6 RMSD between 137 pruned atom pairs is 1.186 angstroms; (across all 308 pairs: 6.559) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.5), sequence alignment score = 1407.4 RMSD between 117 pruned atom pairs is 1.105 angstroms; (across all 308 pairs: 6.707) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.6), sequence alignment score = 1434.4 RMSD between 135 pruned atom pairs is 1.197 angstroms; (across all 308 pairs: 6.156) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.7), sequence alignment score = 1429 RMSD between 122 pruned atom pairs is 1.182 angstroms; (across all 308 pairs: 6.646) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.8), sequence alignment score = 1461.4 RMSD between 145 pruned atom pairs is 1.283 angstroms; (across all 308 pairs: 5.989) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.9), sequence alignment score = 1472.2 RMSD between 135 pruned atom pairs is 1.226 angstroms; (across all 308 pairs: 6.411) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.10), sequence alignment score = 1446.4 RMSD between 119 pruned atom pairs is 1.157 angstroms; (across all 308 pairs: 7.135) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.11), sequence alignment score = 1454.2 RMSD between 143 pruned atom pairs is 1.194 angstroms; (across all 308 pairs: 6.046) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.12), sequence alignment score = 1447.6 RMSD between 151 pruned atom pairs is 1.130 angstroms; (across all 308 pairs: 5.664) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.13), sequence alignment score = 1468.6 RMSD between 156 pruned atom pairs is 1.230 angstroms; (across all 308 pairs: 6.473) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.14), sequence alignment score = 1451.2 RMSD between 163 pruned atom pairs is 1.280 angstroms; (across all 308 pairs: 6.365) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.15), sequence alignment score = 1460.8 RMSD between 133 pruned atom pairs is 1.216 angstroms; (across all 308 pairs: 6.593) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.16), sequence alignment score = 1412.2 RMSD between 139 pruned atom pairs is 1.256 angstroms; (across all 308 pairs: 5.993) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.17), sequence alignment score = 1441 RMSD between 123 pruned atom pairs is 1.130 angstroms; (across all 308 pairs: 6.606) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.18), sequence alignment score = 1460.2 RMSD between 125 pruned atom pairs is 1.189 angstroms; (across all 308 pairs: 6.819) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.19), sequence alignment score = 1429 RMSD between 151 pruned atom pairs is 1.320 angstroms; (across all 308 pairs: 6.077) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fgfr1_03132024_v2.pdb, chain A (#42.20), sequence alignment score = 1442.2 RMSD between 146 pruned atom pairs is 1.244 angstroms; (across all 308 pairs: 6.551) > hide #42.2-20 target m > show : 672,537 > hide atoms > show : 672,537 > color #42.1:MET yellow target c > show : 672,537,651 > hide #11 models > show : 672,537,651,667 > show : 672,537,651,667,645 > show : 672,537,651,667,645,644 > show : 534,538 > show : 534,538,544 > show : 534,538,544,601 > show : 534,538,544,601,757 > show #1 models > hide #1 models Alignment identifier is 1 Alignment identifier is 2 > select > #42.1/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.2/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.3/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.4/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.5/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.6/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.7/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.8/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.9/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.10/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.11/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.12/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.13/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.14/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.15/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.16/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.17/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.18/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.19/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 > #42.20/A:459-462,475-477,522-539,569-572,574-576,581-583,597-617,626-628,648-651,663-666,669-674,679-694,706-715,727-737,747-763 42140 atoms, 42300 bonds, 2540 residues, 20 models selected > show : 534,538,544,601,757,662,706 > show : 534,538,544,601,757,662,706,693 > open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_0.cif Chain information for fold_fgfr1_kd_2p_model_0.cif #43 --- Chain | Description A | . > open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_1.cif Chain information for fold_fgfr1_kd_2p_model_1.cif #44 --- Chain | Description A | . > open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_2.cif Chain information for fold_fgfr1_kd_2p_model_2.cif #45 --- Chain | Description A | . > open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_3.cif Chain information for fold_fgfr1_kd_2p_model_3.cif #46 --- Chain | Description A | . > open /Users/ksinha01/Downloads/fold_fgfr1_kd_2p/fold_fgfr1_kd_2p_model_4.cif Chain information for fold_fgfr1_kd_2p_model_4.cif #47 --- Chain | Description A | . > matchmaker #43-47 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fold_fgfr1_kd_2p_model_0.cif, chain A (#43), sequence alignment score = 1563.4 RMSD between 291 pruned atom pairs is 0.589 angstroms; (across all 308 pairs: 1.618) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fold_fgfr1_kd_2p_model_1.cif, chain A (#44), sequence alignment score = 1557.4 RMSD between 290 pruned atom pairs is 0.385 angstroms; (across all 308 pairs: 1.566) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fold_fgfr1_kd_2p_model_2.cif, chain A (#45), sequence alignment score = 1572.4 RMSD between 292 pruned atom pairs is 0.392 angstroms; (across all 308 pairs: 1.447) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fold_fgfr1_kd_2p_model_3.cif, chain A (#46), sequence alignment score = 1572.4 RMSD between 291 pruned atom pairs is 0.530 angstroms; (across all 308 pairs: 1.480) Matchmaker fold_kd_ctail_2p_model_0.cif, chain A (#11) with fold_fgfr1_kd_2p_model_4.cif, chain A (#47), sequence alignment score = 1574.2 RMSD between 274 pruned atom pairs is 0.643 angstroms; (across all 308 pairs: 1.389) > hide #!42 models > show : 534,538,544,601,757,662,706,693 > show : 534,538,544,601,757,662,706,693 atoms > show #!42 models > hide #!42 models > ui tool show "Renumber Residues" > renumber #43/A #44/A #45/A #46/A #47/A seqStart 458 1540 residues renumbered > renumber #43/A #44/A #45/A #46/A #47/A seqStart 458 0 residues renumbered > show : 534,538,544,601,757,662,706,693 atoms > style #43-47 ball Changed 12285 atom styles > hide #44-47 target m > hide atoms > show #43: 672,651 > show #!42 models > show #42.1: 672,651 > hide #!42 models > show #42.1: 672,651,653,654 > show #43: 672,651,653,654 > show #!42 models > hide #43 models > show #43: 672,651,653,654,706 > show #42.1: 672,651,653,654,706 > hide atoms > close #1-10 > show #43 models > hide #43 models > show #43 models > hide #!42 models > rename #43 id #1 > rename #44 id #2 > rename #45 id #3 > rename #46 id #4 > rename #47 id #5 > showmet Changed 2457 atom styles > distance #1/A:672@CD2 #1/A:713@CD1 Distance between fold_fgfr1_kd_2p_model_0.cif #1/A LEU 672 CD2 and LEU 713 CD1: 3.824Å > show #!21 models > select add #21 42140 atoms, 42300 bonds, 6 pseudobonds, 2540 residues, 22 models selected > show #21.1 models > show #!42 models > hide #1 models > show #42.1:672,651,667 > open 3gqi 3gqi title: Crystal Structure of activated receptor tyrosine kinase in complex with substrates [more info...] Chain information for 3gqi #6 --- Chain | Description | UniProt A | Basic fibroblast growth factor receptor 1 | FGFR1_HUMAN 458-774 B | Phospholipase C-gamma-1 | PLCG1_RAT 545-770 Non-standard residues in 3gqi #6 --- ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β, γ-methylene]triphosphate) DVT — decavanadate MG — magnesium ion > hide #42.1 models > show #42.1 models > matchmaker #6 to #42.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fgfr1_03132024_v2.pdb, chain A (#42.1) with 3gqi, chain A (#6), sequence alignment score = 1449.6 RMSD between 133 pruned atom pairs is 1.191 angstroms; (across all 302 pairs: 6.924) > hide #!42 models > show #!42 models > hide #6/B cartoons > select up 67248 atoms, 67891 bonds, 6 pseudobonds, 4122 residues, 22 models selected > select up 98240 atoms, 99340 bonds, 6 pseudobonds, 6160 residues, 22 models selected > select down 67248 atoms, 67891 bonds, 6 pseudobonds, 4122 residues, 22 models selected > select down 42140 atoms, 42300 bonds, 6 pseudobonds, 2540 residues, 22 models selected > select down 42140 atoms, 42300 bonds, 6 pseudobonds, 2540 residues, 22 models selected > show #6/A:672,651,667 > hide #!42 models > hide atoms > show #6/A:672,651,667 > style #!6 ball Changed 4369 atom styles > label #6/A:672,651,667 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open alphafold_runs_0p_2p.cxs Log from Fri Aug 9 15:07:48 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open alphafold_runs_0p_2p.cxs Log from Thu Aug 8 17:23:41 2024 > alias dd distance delete > alias rd ui mousemode right distance > alias rs ui mousemode right select > alias nmr1 hide #1.2-20 models > alias slall label sel text > "{0.label_one_letter_code}{0.number}{0.insertion_code}" > alias lmearo label #1:thr,met,ala,leu,val,ile,phe,tyr text > "{0.label_one_letter_code}{0.number}{0.insertion_code}" > alias showbb show #1@N,C,CA,O,H; cartoon #1 suppress false; transparency #1 > 50 target c; hide #1:hoh > alias hidebb hide #1@N,C,CA,O,H target a; transparency $1 0 target c > alias sdist ui tool show Distances > alias showmet show #1:ile,leu,val,met,ala,thr target a; hide H; color #1:ile > paleturquoise target a; color #1:leu lightsalmon target a; color #1:val > khaki target a; color #1:met thistle target a; color #1:ala yellowgreen > target ab; color #1:thr aquamarine target a;color byhetero target a ; style > #1 ball > alias showmet2 show #2:ile,leu,val,met,ala,thr target a; hide H; color > #2:ile paleturquoise target a; color #2:leu lightsalmon target a; color > #2:val khaki target a; color #2:met thistle target a; color #2:ala > yellowgreen target ab; color #2:thr aquamarine target a;color byhetero > target a ; style #2 ball > alias showmet3 show #3:ile,leu,val,met,ala,thr target a; hide H; color > #3:ile paleturquoise target a; color #3:leu lightsalmon target a; color > #3:val khaki target a; color #3:met thistle target a; color #3:ala > yellowgreen target ab; color #3:thr aquamarine target a;color byhetero > target a ; style #3 ball > alias showaro show #1:phe,tyr,his,trp target ab; hide H; color #1:phe plum > target a; color #1:tyr lightpink target a; color byhetero target a > ui mousemode right distance > alias fgfr1_brake show #1: 546,562,638 > alias fgfr2_brake show #1: 549,565,641 > alias fgfr3_brake show #1: 540,556,632 > alias fgfr4_brake show #1: 535,551,627 UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open fold_kd_ctail_0p_run_1_model_0.cif Chain information for fold_kd_ctail_0p_run_1_model_0.cif #1 --- Chain | Description A | . > open > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_1/fold_kd_ctail_0p_run_1_model_4.cif Chain information for fold_kd_ctail_0p_run_1_model_1.cif #2 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_1_model_2.cif #3 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_1_model_3.cif #4 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_1_model_4.cif #5 --- Chain | Description A | . > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_1.cif, chain A (#2), sequence alignment score = 1871 RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs: 4.590) > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_2.cif, chain A (#3), sequence alignment score = 1887.8 RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs: 21.274) > matchmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_3.cif, chain A (#4), sequence alignment score = 1881.8 RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs: 8.985) > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_1_model_4.cif, chain A (#5), sequence alignment score = 1871 RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs: 24.527) > open > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_0p_run_2/fold_kd_ctail_0p_run_2_model_4.cif Chain information for fold_kd_ctail_0p_run_2_model_0.cif #6 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_1.cif #7 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_2.cif #8 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_3.cif #9 --- Chain | Description A | . Chain information for fold_kd_ctail_0p_run_2_model_4.cif #10 --- Chain | Description A | . > matchmaker #6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_0.cif, chain A (#6), sequence alignment score = 1887.8 RMSD between 365 pruned atom pairs is 0.000 angstroms; (across all 365 pairs: 0.000) > matchmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_1.cif, chain A (#7), sequence alignment score = 1871 RMSD between 310 pruned atom pairs is 0.487 angstroms; (across all 365 pairs: 4.590) > matchmaker #8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_2.cif, chain A (#8), sequence alignment score = 1887.8 RMSD between 311 pruned atom pairs is 0.433 angstroms; (across all 365 pairs: 21.274) > matchmaker #9 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_3.cif, chain A (#9), sequence alignment score = 1881.8 RMSD between 298 pruned atom pairs is 0.353 angstroms; (across all 365 pairs: 8.985) > matchmaker #10 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_0p_run_2_model_4.cif, chain A (#10), sequence alignment score = 1871 RMSD between 293 pruned atom pairs is 0.324 angstroms; (across all 365 pairs: 24.527) > open /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p/fold_kd_ctail_2p_model_4.cif Chain information for fold_kd_ctail_2p_model_0.cif #11 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_1.cif #12 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_2.cif #13 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_3.cif #14 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_model_4.cif #15 --- Chain | Description A | . > matchmaker #1? to #1 Missing or invalid "matchAtoms" argument: only initial part "#1" of atom specifier valid > matchmaker #11 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_0.cif, chain A (#11), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.401 angstroms; (across all 365 pairs: 28.856) > matchmaker #12 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_1.cif, chain A (#12), sequence alignment score = 1833.8 RMSD between 273 pruned atom pairs is 0.368 angstroms; (across all 365 pairs: 31.133) > matchmaker #13 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_2.cif, chain A (#13), sequence alignment score = 1842.8 RMSD between 265 pruned atom pairs is 0.376 angstroms; (across all 365 pairs: 27.667) > matchmaker #14 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_3.cif, chain A (#14), sequence alignment score = 1842.8 RMSD between 271 pruned atom pairs is 0.446 angstroms; (across all 365 pairs: 28.883) > matchmaker #15 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_model_4.cif, chain A (#15), sequence alignment score = 1833.8 RMSD between 269 pruned atom pairs is 0.368 angstroms; (across all 365 pairs: 28.340) > matchmaker #16 to #1 No molecules/chains to match specified > open > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_2p_run_2/fold_kd_ctail_2p_run_2_model_4.cif Chain information for fold_kd_ctail_2p_run_2_model_0.cif #16 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_1.cif #17 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_2.cif #18 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_3.cif #19 --- Chain | Description A | . Chain information for fold_kd_ctail_2p_run_2_model_4.cif #20 --- Chain | Description A | . > matchmaker #16 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_0.cif, chain A (#16), sequence alignment score = 1821.8 RMSD between 269 pruned atom pairs is 0.342 angstroms; (across all 365 pairs: 29.041) > matchmaker #17 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_1.cif, chain A (#17), sequence alignment score = 1821.8 RMSD between 270 pruned atom pairs is 0.304 angstroms; (across all 365 pairs: 34.580) > matchmaker #18 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_2.cif, chain A (#18), sequence alignment score = 1827.8 RMSD between 269 pruned atom pairs is 0.331 angstroms; (across all 365 pairs: 29.393) > matchmaker #19 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_3.cif, chain A (#19), sequence alignment score = 1863.8 RMSD between 278 pruned atom pairs is 0.415 angstroms; (across all 365 pairs: 13.710) > matchmaker #20 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_2p_run_2_model_4.cif, chain A (#20), sequence alignment score = 1833.8 RMSD between 271 pruned atom pairs is 0.330 angstroms; (across all 365 pairs: 29.597) > ui tool show "Renumber Residues" > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458 7300 residues renumbered > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A seqStart 458 0 residues renumbered > show :771 > hide #1-10 target m > show #1-10 target m > hide #11-20 target m > show :653,654 > show #11-20 target m > hide #1-10 target m > show #1-10 target m > hide #1-10 target m > hide :780-822 > hide :780-822 cartoons > show #1-10 target m > show :695-725 atoms > show :767-779 atoms > hide #1-10 target m > show #1-10 target m > hide #1-10 target m > hide #11-19 target m > color #20:767-779 green target c > color #20:767-779 byelement target a > show :694 atoms > distance #20/A:694@CE1 #20/A:767@CD1 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU 767 CD1: 6.998Å > distance #20/A:694@CE1 #20/A:767@CD2 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A PHE 694 CE1 and LEU 767 CD2: 6.279Å > distance #20/A:696@CD1 #20/A:769@CD1 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU 769 CD1: 2.824Å > distance #20/A:696@CD1 #20/A:769@CD2 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A LEU 696 CD1 and LEU 769 CD2: 4.764Å > ~distance #20/A:696@CD1 #20/A:769@CD2 > distance #20/A:695@CG2 #20/A:773@CD2 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU 773 CD2: 5.040Å > ~distance #20/A:695@CG2 #20/A:773@CD2 > distance #20/A:695@CG2 #20/A:773@CD1 Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A THR 695 CG2 and LEU 773 CD1: 6.542Å > ~distance #20/A:695@CG2 #20/A:773@CD1 > hide :780-822 cartoons > hide :766-822 cartoons > distance #20/A:724@ND2 #20/A:768@O Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and ASP 768 O: 3.574Å > distance #20/A:724@ND2 #20/A:767@O Distance between fold_kd_ctail_2p_run_2_model_4.cif #20/A ASN 724 ND2 and LEU 767 O: 5.063Å > hide :766-822 atoms > save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD- > Ctail/alphafold_runs_0p_2p.pdb > save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD- > Ctail/alphafold_runs_0p_2p.cxs ——— End of log from Thu Aug 8 17:23:41 2024 ——— opened ChimeraX session > open > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_1/fold_kd_ctail_y653p_run_1_model_4.cif Chain information for fold_kd_ctail_y653p_run_1_model_0.cif #22 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_1.cif #23 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_2.cif #24 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_3.cif #25 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_1_model_4.cif #26 --- Chain | Description A | . > matchmaker #22-26 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_0.cif, chain A (#22), sequence alignment score = 1869.8 RMSD between 281 pruned atom pairs is 0.444 angstroms; (across all 365 pairs: 16.950) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_1.cif, chain A (#23), sequence alignment score = 1827.8 RMSD between 269 pruned atom pairs is 0.326 angstroms; (across all 365 pairs: 25.654) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_2.cif, chain A (#24), sequence alignment score = 1833.8 RMSD between 268 pruned atom pairs is 0.334 angstroms; (across all 365 pairs: 27.277) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_3.cif, chain A (#25), sequence alignment score = 1827.8 RMSD between 269 pruned atom pairs is 0.345 angstroms; (across all 365 pairs: 28.333) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_1_model_4.cif, chain A (#26), sequence alignment score = 1830.8 RMSD between 270 pruned atom pairs is 0.353 angstroms; (across all 365 pairs: 27.133) > show #11-20 target m > hide :780-822 cartoons > open > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y653p_run_2/fold_kd_ctail_y653p_run_2_model_4.cif Chain information for fold_kd_ctail_y653p_run_2_model_0.cif #27 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_1.cif #28 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_2.cif #29 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_3.cif #30 --- Chain | Description A | . Chain information for fold_kd_ctail_y653p_run_2_model_4.cif #31 --- Chain | Description A | . > matchmaker #27-31 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_0.cif, chain A (#27), sequence alignment score = 1827.8 RMSD between 268 pruned atom pairs is 0.409 angstroms; (across all 365 pairs: 31.267) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_1.cif, chain A (#28), sequence alignment score = 1842.8 RMSD between 273 pruned atom pairs is 0.458 angstroms; (across all 365 pairs: 31.317) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_2.cif, chain A (#29), sequence alignment score = 1833.8 RMSD between 268 pruned atom pairs is 0.382 angstroms; (across all 365 pairs: 29.220) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_3.cif, chain A (#30), sequence alignment score = 1836.8 RMSD between 266 pruned atom pairs is 0.366 angstroms; (across all 365 pairs: 28.088) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y653p_run_2_model_4.cif, chain A (#31), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.691 angstroms; (across all 365 pairs: 30.898) > ui tool show "Renumber Residues" > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A > #26/A #27/A #28/A #29/A #30/A #31/A seqStart 458 3650 residues renumbered > hide :780-822 cartoons > show :766-780 cartoons > open > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_1/fold_kd_ctail_y654p_run_1_model_4.cif Chain information for fold_kd_ctail_y654p_run_1_model_0.cif #32 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_1.cif #33 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_2.cif #34 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_3.cif #35 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_1_model_4.cif #36 --- Chain | Description A | . > open > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_0.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_1.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_2.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_3.cif > /Users/ksinha01/Downloads/fold_kd_ctail_y654p_run_2/fold_kd_ctail_y654p_run_2_model_4.cif Chain information for fold_kd_ctail_y654p_run_2_model_0.cif #37 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_1.cif #38 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_2.cif #39 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_3.cif #40 --- Chain | Description A | . Chain information for fold_kd_ctail_y654p_run_2_model_4.cif #41 --- Chain | Description A | . > matchmaker #32-41 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_0.cif, chain A (#32), sequence alignment score = 1830.8 RMSD between 274 pruned atom pairs is 0.339 angstroms; (across all 365 pairs: 30.830) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_1.cif, chain A (#33), sequence alignment score = 1833.8 RMSD between 273 pruned atom pairs is 0.367 angstroms; (across all 365 pairs: 29.517) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_2.cif, chain A (#34), sequence alignment score = 1833.8 RMSD between 275 pruned atom pairs is 0.503 angstroms; (across all 365 pairs: 33.883) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_3.cif, chain A (#35), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.398 angstroms; (across all 365 pairs: 28.779) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_1_model_4.cif, chain A (#36), sequence alignment score = 1842.8 RMSD between 265 pruned atom pairs is 0.443 angstroms; (across all 365 pairs: 28.961) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_0.cif, chain A (#37), sequence alignment score = 1827.8 RMSD between 274 pruned atom pairs is 0.440 angstroms; (across all 365 pairs: 30.375) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_1.cif, chain A (#38), sequence alignment score = 1833.8 RMSD between 272 pruned atom pairs is 0.466 angstroms; (across all 365 pairs: 31.050) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_2.cif, chain A (#39), sequence alignment score = 1833.8 RMSD between 274 pruned atom pairs is 0.336 angstroms; (across all 365 pairs: 29.924) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_3.cif, chain A (#40), sequence alignment score = 1833.8 RMSD between 271 pruned atom pairs is 0.449 angstroms; (across all 365 pairs: 28.353) Matchmaker fold_kd_ctail_0p_run_1_model_0.cif, chain A (#1) with fold_kd_ctail_y654p_run_2_model_4.cif, chain A (#41), sequence alignment score = 1833.8 RMSD between 270 pruned atom pairs is 0.399 angstroms; (across all 365 pairs: 32.127) > hide :780-822 cartoons > ui tool show "Renumber Residues" > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A > #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A > #38/A #39/A #40/A #41/A seqStart 458 3650 residues renumbered > renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A > #13/A #14/A #15/A #16/A #17/A #18/A #19/A #20/A #22/A #23/A #24/A #25/A > #26/A #27/A #28/A #29/A #30/A #31/A #32/A #33/A #34/A #35/A #36/A #37/A > #38/A #39/A #40/A #41/A seqStart 458 0 residues renumbered > hide :780-822 cartoons > hide cartoons > hide atoms > show :695-725 cartoons > show #1-10 target m > show :695-725 atoms > hide #1-10 target m > coulombic #41:720 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue PTR (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2 -fi mol2 -o /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmp3jkz2bjg/ante.in.mol2); atoms read (36), bonds read (36).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 166; net charge: -2` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface #41.1: minimum, -14.09, mean -2.42, maximum 12.27 > coulombic #41:695-725 Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface #41.1: minimum, -14.09, mean -2.42, maximum 12.27 > show :766-780 cartoons > hide #!41 models > show #!41 models > hide #!41 models > coulombic #40:766-780 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue PTR (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2 -fi mol2 -o /var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 -dr n (PTR) `` (PTR) `Welcome to antechamber 20.0: molecular input file processor.` (PTR) `` (PTR) `Info: Finished reading file (/var/folders/gf/77wjbg8d251f7qwfdl_zvz840000gp/T/tmpvhy3326u/ante.in.mol2); atoms read (34), bonds read (34).` (PTR) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (PTR) `` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (PTR) `Info: Total number of electrons: 164; net charge: -2` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (PTR) `` (PTR) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (PTR) `` Charges for residue PTR determined Coulombic values for fold_kd_ctail_y654p_run_2_model_3.cif_A SES surface #40.1: minimum, -13.70, mean -2.40, maximum 12.19 > show #!41 models > coulombic #41:766-780 Coulombic values for fold_kd_ctail_y654p_run_2_model_4.cif_A SES surface #41.1: minimum, -14.09, mean -2.42, maximum 12.27 > hide #11-20,22-39#!40-41 surfaces > show :458-780 cartoons > show #1-10 target m > show :653,654 atoms > hide #1-10 target m > hide #11-20 target m > show #11-20 target m > hide #22-31 target m > hide #32-39#!40-41 target m > show #11-20 target m > show #22-39#!40 target m > hide #12 models > show #12 models > hide #11 models > show #11 models > hide #14 models > show #14 models > hide #16 models > show #16 models > hide #22 models > hide #19 models > hide #12-39#!40-41 target m > show #1-10 target m > hide #1-10 target m > save /Users/ksinha01/Kinases_local/FGFR1/FGFR1_KD- > Ctail/alphafold_runs_0p_2p.cxs ——— End of log from Fri Aug 9 15:07:48 2024 ——— opened ChimeraX session > label #6/A:672,651,667 > label #6/A:672,651,667,671,668 > label #11:672,651,667,671,668 OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,1 Processor Name: 10-Core Intel Core i9 Processor Speed: 3.6 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache (per Core): 256 KB L3 Cache: 20 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 580.140.1~8 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 13 days, 15 hours, 48 minutes Graphics/Displays: AMD Radeon Pro 5300: Chipset Model: AMD Radeon Pro 5300 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0047 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XL-012 Option ROM Version: 113-D322A1XL-012 EFI Driver Version: 01.01.231 Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG Ultra HD: Resolution: 6720 x 3780 UI Looks like: 3360 x 1890 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 14 months ago
Component: | Unassigned → Window Toolkit |
---|---|
Description: | modified (diff) |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 14 months ago
Resolution: | → duplicate |
---|---|
Status: | assigned → closed |
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Qt 6.6 crash in displayConfigFinalizedProc() either connecting or disconnecting a display or waking from sleep.