id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18251 Crash opening .cif chimerax-bug-report@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003587bb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 320 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 765 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 768 in get File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1678 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/tasks.py"", line 300 in _run_function File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003577af000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003567a3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000355797000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000035478b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000035377f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000352773000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000351767000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000035075b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034f74f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034e743000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034d737000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034c72b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034b71f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000034a713000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000349707000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py"", line 962 in getaddrinfo File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/connection.py"", line 60 in create_connection File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py"", line 199 in _new_conn File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py"", line 279 in connect File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 979 in send File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1041 in _send_output File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1281 in endheaders File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py"", line 441 in request File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py"", line 495 in _make_request File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py"", line 789 in urlopen File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/poolmanager.py"", line 443 in urlopen File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/_request_methods.py"", line 182 in request_encode_url File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/_request_methods.py"", line 135 in request File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/rest.py"", line 206 in request File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/rest.py"", line 228 in GET File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/api_client.py"", line 341 in request File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/api_client.py"", line 151 in __call_api File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 125 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003484ff000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py"", line 1134 in read File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py"", line 1278 in recv_into File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py"", line 706 in readinto File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 279 in _read_status File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 318 in begin File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1378 in getresponse File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 1352 in do_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 1391 in https_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 496 in _call_chain File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 536 in _open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 519 in open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 216 in urlopen File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/available.py"", line 62 in load File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 516 in reload_available File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000020d1f1f00 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py"", line 54 in open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 497 in remember_data_format File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 526 in collated_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 215 in provider_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 132 in cmd_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 2117 in _open_dropped_file File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 293 in event File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, 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not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/keshavkishor/Desktop/MGAT6/mgat4c.pdb Chain information for mgat4c.pdb #1 --- Chain | Description A | No description available > select ::name=""L01""::name=""L02""::name=""MN"" 144 atoms, 152 bonds, 3 residues, 1 model selected > show sel target ab > style sel ball Changed 144 atom styles > color sel byhetero > color sel lime > color sel cyan > color sel byhetero > select clear > hide atoms > show atoms > hide cartoons > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 3734 atoms, 3832 bonds, 464 residues, 1 model selected > hide sel atoms > style sel stick Changed 3734 atom styles Drag select of 144 atoms, 152 bonds > style sel stick Changed 144 atom styles > style sel sphere Changed 144 atom styles > style sel ball Changed 144 atom styles > style sel stick Changed 144 atom styles > set bgColor white > set bgColor black > set bgColor white > lighting soft > lighting full > lighting simple > ui tool show ""Selection Inspector"" > view sel > select clear > close > open /Users/keshavkishor/Desktop/MGAT6/mgat4c.pdb format pdb Chain information for mgat4c.pdb #1 --- Chain | Description A | No description available > select /A 3734 atoms, 3832 bonds, 464 residues, 1 model selected > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 3734 atoms, 3832 bonds, 464 residues, 1 model selected > hide sel atoms > select ::name=""MN"" 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > select ::name=""L01"" 104 atoms, 111 bonds, 1 residue, 1 model selected > color sel cyan > color sel byhetero > style sel ball Changed 104 atom styles > style sel stick Changed 104 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > select ::name=""L01"" 104 atoms, 111 bonds, 1 residue, 1 model selected > select ::name=""L02"" 39 atoms, 41 bonds, 1 residue, 1 model selected > color sel hot pink > color sel byhetero > select clear > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 3734 atoms, 3832 bonds, 464 residues, 1 model selected > show sel surfaces > hide sel surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select clear > select /A:210 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:210-212 25 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > label (#!1 & sel) attribute name > style sel ball Changed 25 atom styles > style sel stick Changed 25 atom styles > select clear > save /Users/keshavkishor/Desktop/MGAT6/mgatc4c.pdb serialNumbering amber > open /Users/keshavkishor/Desktop/MGAT6/Try/N-glycan.pdb > /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb Chain information for mgat4c_v2.pdb #3 --- Chain | Description A | No description available Computing secondary structure > close #1 > hide #3 models > select all 4079 atoms, 4190 bonds, 476 residues, 2 models selected > select H 97 atoms, 9 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #2/?:4@O6 1 atom, 1 residue, 1 model selected > select add #2/?:7@C1 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select clear > select add #3 3878 atoms, 3984 bonds, 467 residues, 1 model selected > select add #2 3982 atoms, 4094 bonds, 476 residues, 2 models selected > matchmaker #2 to #3 No matrix compatible with both reference structure and all match structures > show #3 models > open 5vcm fromDatabase uniprot_variants format variants Fetching url https://www.ebi.ac.uk/proteins/api/variation/5vcm failed: HTTP Error 400: Bad Request > close #2 > hide sel cartoons > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 3734 atoms, 3832 bonds, 464 residues, 1 model selected > hide sel atoms > view sel No displayed objects specified. > show sel cartoons > select clear > ui tool show ViewDockX No suitable models found for ViewDockX > hide cartoons Drag select of 104 atoms, 111 bonds > delete sel > show cartoons > save /Users/keshavkishor/Desktop/MGAT6/Try/receptor.pdb relModel #3 > open /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb Chain information for mgat4c_v2.pdb #1 --- Chain | Description A | No description available Computing secondary structure > hide #1 models > show #1 models > hide #3 models > hide #1 cartoons > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 7468 atoms, 7664 bonds, 928 residues, 2 models selected > hide sel & #1 atoms > show #3 models > show sel surfaces > hide sel surfaces > show sel surfaces > hide sel surfaces > open /Users/keshavkishor/Desktop/MGAT6/Try/output_models.pdbqt Summary of feedback from opening /Users/keshavkishor/Desktop/MGAT6/Try/output_models.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -5.7 0.000 0.000 Ignored bad PDB record found on line 3 REMARK WARNING: 32 MAX_TORS EXCEEDED!!! Ignored bad PDB record found on line 5 REMARK status: ('A' for Active; 'I' for Inactive) Ignored bad PDB record found on line 6 REMARK 1 A between atoms: O1_2 and C1_3 Ignored bad PDB record found on line 7 REMARK 2 A between atoms: C5_5 and C6_6 2995 messages similar to the above omitted Opened output_models.pdbqt containing 20 structures (2600 atoms, 2560 bonds) > viewdockx #2.1-20 > hide sel cartoons > hide #!2 models > show #!2 models > hide #!2 models > hide #2.1 models > show #2.1 models > hide #2.1-20#!3 target m > select add #2 10068 atoms, 10224 bonds, 1208 residues, 25 models selected > show #2.1 models > show #2.2 models Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. > hide #2.2 models Cell requested for row 0 is out of bounds for table with 0 rows! Resizing table model. > show #2.2 target m > hide #2.1 target m > show #2.3 target m > hide #2.2 target m > show #2.4 target m > hide #2.3 target m > show #2.5 target m > hide #2.4 target m > show #2.6 target m > hide #2.5 target m > show #2.7 target m > hide #2.6 target m > show #2.8 target m > hide #2.7 target m > show #2.9 target m > hide #2.8 target m > show #2.10 target m > hide #2.9 target m > show #2.11 target m > hide #2.10 target m > show #2.12 target m > hide #2.11 target m > show #2.13 target m > hide #2.12 target m > show #2.14 target m > hide #2.13 target m > show #2.15 target m > hide #2.14 target m > show #2.16 target m > hide #2.15 target m > show #2.17 target m > hide #2.16 target m > show #2.18 target m > hide #2.17 target m > show #2.19 target m > hide #2.18 target m > show #2.20 target m > hide #2.19 target m > show #2.19 target m > hide #2.20 target m > show #2.20 target m > hide #2.19 target m > show #!3 target m > hide #2.20 target m > show #2.1 target m > hide #!3 target m Cell requested for row 1 is out of bounds for table with 23 rows! Resizing table model. > hide #!2 models > select subtract #2 7468 atoms, 7664 bonds, 928 residues, 4 models selected > open /Users/keshavkishor/Desktop/MGAT6/Try/ligand.pdb Cell requested for row 1 is out of bounds for table with 4 rows! Resizing table model. > select add #4 7669 atoms, 7870 bonds, 937 residues, 5 models selected Drag select of 74 atoms, 80 bonds > select clear Drag select of 104 atoms, 111 bonds > display H sel > show H sel Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show H sel Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show H > show sel target ab > select clear Drag select of 201 atoms, 206 bonds > select H 617 atoms, 249 residues, 21 models selected > delete atoms (#4 & sel) > delete bonds (#4 & sel) > select #4/?:9@C1 1 atom, 1 residue, 1 model selected > select add #4/?:7@O6 2 atoms, 2 residues, 1 model selected > bond sek Missing or invalid ""atoms"" argument: invalid atoms specifier > bond sel Created 1 bond > select clear > select #4/?:7@C1 1 atom, 1 residue, 1 model selected > select add #4/?:4@O6 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > select clear > open > /Users/keshavkishor/Desktop/MGAT6/Try/72e2a1c9-3a4d-485e-ab96-1009f48b987b/all.pdb Summary of feedback from opening /Users/keshavkishor/Desktop/MGAT6/Try/72e2a1c9-3a4d-485e-ab96-1009f48b987b/all.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY Re-Glyco from GlycoShape Ignored bad PDB record found on line 2 REMARK Time 2025-07-22-14:06:15 Ignored bad PDB record found on line 3 REMARK ______ _______ _______ ___ __ __ _______ _______ Ignored bad PDB record found on line 5 REMARK| | || | ___| ____ | ___|| | | |_| || || _ | Ignored bad PDB record found on line 6 REMARK| |_||_ | |___ |____| | | __ | | | || || | | | 611 messages similar to the above omitted Chain information for all.pdb --- Chain | Description 5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A 5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A 5.21/A 5.22/A 5.23/A 5.24/A 5.25/A 5.26/A 5.27/A 5.28/A 5.29/A 5.30/A 5.31/A 5.32/A 5.33/A 5.34/A 5.35/A 5.36/A 5.37/A 5.38/A 5.39/A 5.40/A 5.41/A 5.42/A 5.43/A 5.44/A 5.45/A 5.46/A 5.47/A 5.48/A 5.49/A 5.50/A | No description available Computing secondary structure > hide #4 models > hide #!1 models > select all 199856 atoms, 204928 bonds, 24522 residues, 75 models selected > show sel & #5.1-50 cartoons > select > ::name=""0YB""::name=""2MA""::name=""4YB""::name=""L01""::name=""L02""::name=""MN""::name=""ROH""::name=""VMB""::name=""XMA"" 5688 atoms, 5664 bonds, 394 residues, 73 models selected > show sel & #5.1-50 atoms > close #5 > show #4 models > show #!3 models > show #!2 models > show #!1 models Cell requested for row 1 is out of bounds for table with 5 rows! Resizing table model. > close #2 > close #1 > select all 3878 atoms, 3984 bonds, 475 residues, 2 models selected > show sel cartoons > open /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb Chain information for mgat4c_v2.pdb #1 --- Chain | Description A | No description available Computing secondary structure > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 7468 atoms, 7664 bonds, 928 residues, 2 models selected > hide sel atoms > show sel cartoons > hide sel cartoons Drag select of 80 atoms, 82 bonds > hide sel atoms Drag select of 104 atoms, 111 bonds Drag select of 2 bonds Drag select of 104 atoms, 111 bonds > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" Drag select of 5 atoms, 8 bonds Drag select of 104 atoms, 111 bonds > ui mousemode right ""translate selected models"" Drag select of 3 atoms, 4 bonds Drag select of 104 atoms, 111 bonds > select clear > hide #!3 models > close #3 Drag select of 104 atoms, 111 bonds > save /Users/keshavkishor/Desktop/MGAT6/Try/n-glycan_alphafold.pdb > selectedOnly true Computing secondary structure > open /Users/keshavkishor/Desktop/MGAT6/Try/n-glycan_alphafold.pdb Summary of feedback from opening /Users/keshavkishor/Desktop/MGAT6/Try/n-glycan_alphafold.pdb --- warnings | Cannot find LINK/SSBOND residue ROH (1 ) Cannot find LINK/SSBOND residue 4YB (2 ) Cannot find LINK/SSBOND residue 4YB (3 ) Cannot find LINK/SSBOND residue VMB (4 ) Cannot find LINK/SSBOND residue 2MA (5 ) 3 messages similar to the above omitted > select add #1 3878 atoms, 3984 bonds, 467 residues, 1 model selected > select subtract #1 Nothing selected > hide #1 models > close #1 > tile 2 models tiled > select ~sel & ##selected Nothing selected > ~tile > select #4/?:2@C1 1 atom, 1 residue, 1 model selected > select add #4/?:2@C2 2 atoms, 1 residue, 1 model selected > select add #4/?:2@C3 3 atoms, 1 residue, 1 model selected > select add #4/?:2@C4 4 atoms, 1 residue, 1 model selected > select add #4/?:2@C5 5 atoms, 1 residue, 1 model selected > select add #4/?:2@C6 6 atoms, 1 residue, 1 model selected > select add #4/?:2@O6 7 atoms, 1 residue, 1 model selected > select add #2/C:1@C5 8 atoms, 2 residues, 2 models selected > select subtract #2/C:1@C5 7 atoms, 1 residue, 1 model selected > select add #2/C:1@C7 8 atoms, 2 residues, 2 models selected > select add #2/C:1@C3 9 atoms, 2 residues, 2 models selected > select add #2/C:1@C4 10 atoms, 2 residues, 2 models selected > select add #2/C:1@C5 11 atoms, 2 residues, 2 models selected > select add #2/C:1@C6 12 atoms, 2 residues, 2 models selected > select add #2/C:1@C8 13 atoms, 2 residues, 2 models selected > select add #2/C:1@O4 14 atoms, 2 residues, 2 models selected > matchmaker #2to #4 sel Missing or invalid ""matchAtoms"" argument: only initial part ""#2"" of atom specifier valid > matchmaker #2 to #4 sel Expected a keyword > matchmaker #2:sel to #4:sel No 'to' model specified > align #2:sel toAtoms #4:sel No atoms paired for alignment > align #2:C,N,O toAtoms #4:C,N,O No atoms paired for alignment > cofr #2 > select clear Drag select of 104 atoms, 111 bonds > view matrix models > #4,0.96143,-0.27435,0.019454,-0.071193,0.14538,0.44686,-0.88271,-30.98,0.23348,0.8515,0.46951,-43.27 > view matrix models > #4,0.96143,-0.27435,0.019454,-2.4603,0.14538,0.44686,-0.88271,-29.436,0.23348,0.8515,0.46951,-44.862 > ui mousemode right rotate Drag select of 1 atoms > view sel > hide #2 models > show #2 models > hide #4 models > select add #4 104 atoms, 111 bonds, 9 residues, 1 model selected > show #4 models > ui mousemode right ""rotate selected models"" > select clear > select #2 104 atoms, 111 bonds, 1 residue, 1 model selected > select subtract #2 Nothing selected > hide #2 models > select add #4 104 atoms, 111 bonds, 9 residues, 1 model selected > view matrix models > #4,0.96635,-0.25563,0.028492,-2.7695,0.15932,0.50791,-0.84655,-30.367,0.20193,0.82261,0.53155,-43.51 > view matrix models > #4,0.96904,-0.23845,0.064085,-2.8705,0.18131,0.51101,-0.84023,-30.804,0.1676,0.82584,0.53843,-42.851 > ui mousemode right ""move picked models"" > show #2 models > select add #2 208 atoms, 222 bonds, 10 residues, 2 models selected > select subtract #2 104 atoms, 111 bonds, 9 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #4,0.96904,-0.23845,0.064085,-3.3232,0.18131,0.51101,-0.84023,-30.945,0.1676,0.82584,0.53843,-43.173 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.79164,-0.39213,-0.46856,-0.5965,0.27999,0.91444,-0.29223,-35.561,0.54306,0.10015,0.8337,-38.701 > view matrix models > #4,0.88137,-0.43839,-0.17608,-0.11339,0.30552,0.8132,-0.49534,-35.733,0.36034,0.38278,0.85067,-39.023 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.88137,-0.43839,-0.17608,-1.2122,0.30552,0.8132,-0.49534,-35.012,0.36034,0.38278,0.85067,-39.816 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.76939,-0.49904,-0.39875,0.6116,0.38331,0.86004,-0.33675,-36.324,0.51099,0.10625,0.85299,-38.853 > view matrix models > #4,0.869,-0.49447,-0.018558,0.66358,0.41378,0.74673,-0.52075,-36.32,0.27135,0.44485,0.85351,-38.942 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.869,-0.49447,-0.018558,0.20345,0.41378,0.74673,-0.52075,-36.204,0.27135,0.44485,0.85351,-39.273 > select clear > close #2 > open /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb Chain information for mgat4c_v2.pdb #1 --- Chain | Description A | No description available Computing secondary structure > close #1 > open /Users/keshavkishor/Desktop/MGAT6/mgat4c.pdb Chain information for mgat4c.pdb #1 --- Chain | Description A | No description available > select > ::name=""0YB""::name=""2MA""::name=""4YB""::name=""L01""::name=""L02""::name=""MN""::name=""ROH""::name=""VMB""::name=""XMA"" 248 atoms, 263 bonds, 12 residues, 2 models selected > show sel target ab > view matrix models > #4,0.869,-0.49447,-0.018558,8.3209,0.41378,0.74673,-0.52075,-34.067,0.27135,0.44485,0.85351,-59.663,#1,1,0,0,8.1174,0,1,0,2.137,0,0,1,-20.39 > view matrix models > #4,0.869,-0.49447,-0.018558,11.644,0.41378,0.74673,-0.52075,-35.206,0.27135,0.44485,0.85351,-64.232,#1,1,0,0,11.44,0,1,0,0.99771,0,0,1,-24.96 > hide sel cartoons Drag select of 403 atoms, 400 bonds, 454 residues > hide sel cartoons Drag select of 484 atoms, 492 bonds, 10 residues > hide sel cartoons > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 3734 atoms, 3832 bonds, 464 residues, 1 model selected > hide sel atoms > view matrix models #1,1,0,0,3.4443,0,1,0,-7.6297,0,0,1,-33.244 > undo > select clear Drag select of 40 atoms, 41 bonds > hide sel atoms > view matrix models #1,1,0,0,8.1148,0,1,0,5.1281,0,0,1,-11.119 > undo > select clear Drag select of 104 atoms, 111 bonds > view matrix models > #4,0.869,-0.49447,-0.018558,-8.2426,0.41378,0.74673,-0.52075,-31.047,0.27135,0.44485,0.85351,-13.652 > view sel > view matrix models > #4,0.869,-0.49447,-0.018558,-5.1187,0.41378,0.74673,-0.52075,-29.845,0.27135,0.44485,0.85351,-16.006 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.29976,-0.36158,-0.88284,-0.5874,0.87669,0.46936,0.10543,-31.57,0.37625,-0.80558,0.45769,-2.6517 > view matrix models > #4,0.22894,-0.14589,-0.96245,-2.6647,0.95735,0.21279,0.19548,-29.055,0.17628,-0.96615,0.18838,2.0299 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.22894,-0.14589,-0.96245,-2.6535,0.95735,0.21279,0.19548,-29.109,0.17628,-0.96615,0.18838,1.9173 > view matrix models > #4,0.22894,-0.14589,-0.96245,-0.11983,0.95735,0.21279,0.19548,-32.355,0.17628,-0.96615,0.18838,-7.6471 > view matrix models > #4,0.22894,-0.14589,-0.96245,1.8764,0.95735,0.21279,0.19548,-31.875,0.17628,-0.96615,0.18838,-5.943 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.23212,-0.16177,-0.95914,2.055,0.9579,0.20929,0.19653,-31.831,0.16895,-0.96438,0.20354,-5.7437 > view matrix models > #4,0.24008,-0.20435,-0.949,2.552,0.95926,0.19995,0.19962,-31.71,0.14896,-0.95826,0.24403,-5.2228 > view matrix models > #4,0.24192,-0.2149,-0.9462,2.6792,0.95956,0.19764,0.20045,-31.679,0.14393,-0.95643,0.25402,-5.0969 > ui mousemode right ""move picked models"" > undo > ui mousemode right ""translate selected models"" > view matrix models > #4,0.24008,-0.20435,-0.949,3.7429,0.95926,0.19995,0.19962,-31.437,0.14896,-0.95826,0.24403,-4.843 > view sel > view matrix models > #4,0.24008,-0.20435,-0.949,3.6817,0.95926,0.19995,0.19962,-31.471,0.14896,-0.95826,0.24403,-5.8141 > view matrix models > #4,0.24008,-0.20435,-0.949,3.6549,0.95926,0.19995,0.19962,-31.479,0.14896,-0.95826,0.24403,-5.9146 > view matrix models > #4,0.24008,-0.20435,-0.949,3.2402,0.95926,0.19995,0.19962,-31.567,0.14896,-0.95826,0.24403,-5.7042 > ui mousemode right rotate > ui mousemode right ""translate selected models"" > view matrix models > #4,0.24008,-0.20435,-0.949,1.0042,0.95926,0.19995,0.19962,-34.5,0.14896,-0.95826,0.24403,-5.5825 > select clear > select #2 Nothing selected > select #4 104 atoms, 111 bonds, 9 residues, 1 model selected > view matrix models > #4,0.24008,-0.20435,-0.949,0.48683,0.95926,0.19995,0.19962,-35.534,0.14896,-0.95826,0.24403,-4.9841 > view matrix models > #4,0.24008,-0.20435,-0.949,3.7318,0.95926,0.19995,0.19962,-36.915,0.14896,-0.95826,0.24403,-4.6404 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.89817,-0.31134,0.31041,-0.75709,0.28021,0.94945,0.14149,-34.546,-0.33877,-0.0401,0.94001,-4.284 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.89817,-0.31134,0.31041,-0.5477,0.28021,0.94945,0.14149,-34.657,-0.33877,-0.0401,0.94001,-4.2497 > ui mousemode right rotate > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.90633,-0.29414,0.30339,-0.98509,0.26344,0.95467,0.13856,-34.421,-0.33039,-0.045652,0.94274,-4.3198 > view matrix models > #4,0.88807,-0.33142,0.31858,-0.026101,0.29982,0.9429,0.14511,-34.927,-0.34848,-0.033353,0.93672,-4.1735 > select clear > hide #1 models Drag select of 72 atoms, 79 bonds Drag select of 2 atoms, 1 bonds Drag select of 1 atoms, 1 bonds > show #1 models > view matrix models > #4,0.90883,-0.30588,0.28366,-0.97535,0.29466,0.95203,0.082552,-35.292,-0.2953,0.0085574,0.95536,-5.693 > select clear > open /Users/keshavkishor/Desktop/MGAT6/with_only_Mn/protein.pdb Chain information for protein.pdb #2 --- Chain | Description A | No description available Computing secondary structure > hide #1 models > hide #2 models > hide #4 models > select add #2 3735 atoms, 3834 bonds, 465 residues, 1 model selected > view sel > show #2 models > view sel > view matrix models > #2,0.84168,-0.099193,0.53079,-0.27156,0.095195,0.99484,0.034964,0.33266,-0.53152,0.0211,0.84678,-1.8373 > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""CYX""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 7468 atoms, 7666 bonds, 928 residues, 2 models selected > hide sel & #2 atoms > select add #1 7612 atoms, 7818 bonds, 931 residues, 2 models selected > select subtract #1 3734 atoms, 3834 bonds, 464 residues, 1 model selected > select clear > open /Users/keshavkishor/Desktop/MGAT6/mgat4c.cif ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: MRX43LL/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 3 days, 56 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: VX3418-2KPC: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 180.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AllMetal3D: 0.8 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 fsspec: 2025.5.1 funcparserlib: 2.0.0a0 glfw: 2.8.0 gradio_client: 0.11.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 hf-xet: 1.1.3 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 huggingface-hub: 0.32.5 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 narwhals: 1.30.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 2.2.3 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 plotly: 6.0.0 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.7.3 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 PyYAML: 6.0.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 Send2Trash: 1.8.3 SEQCROW: 1.8.21 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tomli: 2.0.1 tornado: 6.4.2 tqdm: 4.67.1 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 websockets: 11.0.3 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Input/Output can't reproduce all ChimeraX