id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19872 Crash drawing Qt widget chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x00000004a943b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a842f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a7423000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a6417000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a540b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a43ff000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a33f3000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a23e7000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a13db000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000004a03cf000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049f3c3000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049e3b7000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049d3ab000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049c39f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049b393000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049a387000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049937b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049836f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000497363000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000496357000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049534b000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000049433f000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000493333000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000492327000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File 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128K 2 dyld private memory 432K 5 mapped file 644.7M 98 page table in kernel 11.3M 1 shared memory 3728K 28 =========== ======= ======= TOTAL 19.4G 9309 TOTAL, minus reserved VM space 19.1G 9309 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""255fd96d84b3c4ed8c6375b9506ed111c6618c53"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645eb1d0417dab722a215927"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""68095e8ecb2a9d1eaa8463c9"", ""factorPackIds"" : [ ""68bf4eacb556ea03e19aed49"" ], ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 9i05 fromDatabase pdb format mmcif Summary of feedback from opening 9i05 fetched from pdb --- warnings | Atom H is not in the residue template for PRO /Xo:731 Atom H1 is not in the residue template for UNK /Uf:1 notes | Fetching compressed mmCIF 9i05 from http://files.rcsb.org/download/9i05.cif Fetching CCD FES from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/FES/FES.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 9i05 title: Cryo-EM structure of the large subunit of the mitochondrial ribosome from Toxoplasma gondii [more info...] Chain information for 9i05 #1 --- Chain | Description | UniProt AA | Putative 60S ribosomal protein L27 | A0A7J6JYF7_TOXGO 30-126 AB | Large ribosomal subunit protein mL43 | A0A7J6KC95_TOXGO 1-203 AC | Ribosomal protein L46 | A0A7J6JX23_TOXGO 1-598 AD | Large ribosomal subunit protein mL49 | A0A7J6JUD4_TOXGO 1-310 AE | mL53 | A0A7J6JX69_TOXGO -98-118 AF | Large ribosomal subunit protein mL54 | S8F6A8_TOXGM -384-130 AG | BIR protein | A0A7J6K0B0_TOXGO 1-271 AH | mL102 | A0A0F7V869_TOXGV -360-35 AI | RAP domain-containing protein | A0A7J6KFM0_TOXGO 1-656 Aa | Putative LSU ribosomal protein L2P | A0A7J6KET1_TOXGO -215-362 Ab | Large ribosomal subunit protein uL3m | A0A2G8Y818_TOXGO 1-514 Ac | Large ribosomal subunit protein uL4m | A0A151HQQ9_TOXGO 1-802 Ad | HECT-domain (Ubiquitin-transferase) domain-containing protein | A0A7J6K7T4_TOXGO -111-280 Ae | Ribosomal protein L9, N-terminal domain-containing protein | A0A086JV44_TOXGO 1-492 Af | Putative ribosomal protein L11 | A0A7J6KEF6_TOXGO 1-180 Ag | Putative 50S ribosomal protein L13 | A0A7J6K0U2_TOXGO 1-231 Ah | Putative LSU ribosomal protein L14P | A0A7J6K196_TOXGO 1-122 Ai | Ribosomal protein L15, putative | S8GIU7_TOXGM 1-638 Aj | Putative 50S ribosomal protein L16 | A0A7J6K7Z7_TOXGO 1-187 Ak | Putative 50S ribosomal protein L17 | A0A7J6KEY9_TOXGO 1-247 Al | 50S ribosomal protein L19, chloroplastic | A0A7J6JZ22_TOXGO 0-743 Am | Putative ribosomal protein L20 | B9PY19_TOXGO 1-121 An | Large ribosomal subunit protein bL21m | A0A7J6K7U7_TOXGO 1-679 Ao | Ribosomal L22p/L17e protein | S8F1I2_TOXGM -225-347 Ap | Large ribosomal subunit protein uL23m | A0A7J6K299_TOXGO 1-253 Aq | Large ribosomal subunit protein uL24c | A0A7J6JXG2_TOXGO 1-438 Ar | Ribosomal l25 family protein | S8ER88_TOXGM 1-739 As | bL27m | S8GME4_TOXGM 1-391 At | Putative ribosomal protein L28 | A0A7J6K129_TOXGO 1-282 Au | Large ribosomal subunit protein uL29m | A0A7J6K1F8_TOXGO 1-236 Av | bL32m | A0A7J6K9L3_TOXGO 1-88 Aw | Putative 50S ribosomal protein L33 | A0A7J6JWI3_TOXGO 1-126 Ax | bL35m | A0A7J6KEG8_TOXGO 1-352 Ay | bL36m | A0A3R8AVZ6_TOXGO 1-200 Az | mL40 | A0A7J6KCG7_TOXGO 1-293 RA | LSU-2 | RB | LSU-3 | RC | LSU-4 | RD | LSU-5 | RE | LSU-6 | RF | LSU-7 | RG | LSU-8 | RI | LSU-9 | RJ | LSU-10 | RK | LSU-11 | RL | LSU-12 | RM | LSU-13 | RN | LSU-14 | RO | LSU-15 | RP | LSU-16 | RQ | LSU-17 | RS | LSU-18 | RT | LSU-19 | RU | LSU-20 | RV | LSU-21 | RW | LSU-22 | RX | LSU-23 | RY | LSU-24 | RZ | LSU-25 | Ra | LSU-26 | Rb | LSU-27 | Rc | LSU-28 | Rd | LSU-29 | Rf | LSU-30 | Rg | LSU-31 | Rh | LSU-32 | Ri | LSU-32 | Ua | Ribosomal l25 family protein | A0A7J6JXW0_TOXGO 0-25 Ub | Chain Uc | Uc | Chain Ud | Ud | Chain Ue | Ue | Chain Uf | Uf | LSU-1 | XA | mL155 | A0A7J6KDX2_TOXGO -223-86 XB | mL156 | A0A7J6K9K6_TOXGO -94-103 XC | mL157 | A0A7J6JWE1_TOXGO 1-305 XD | mL158 | S7UHA3_TOXGG -19-216 XE | mL159 | A0A7J6KA70_TOXGO 1-150 XF | mL160 | A0A7J6JZI4_TOXGO 1-141 XG | mL161 | A0A7J6K5D7_TOXGO -445-30 XH | Ribosomal protein RPL22 | A0A7J6JUA9_TOXGO -159-181 XI | Transmembrane protein | A0A7J6K730_TOXGO -166-35 XJ | Chain Ua | Xa | mL130 | A0A7J6JZ23_TOXGO -362-181 Xb | RRM domain-containing protein | S7UYV0_TOXGG 1-664 Xc | mL132 | A0A7J6JXX9_TOXGO 1-198 Xd | RAP domain-containing protein | A0A2G8XP01_TOXGO 1-927 Xe | Large ribosomal subunit protein uL24c | A0A7J6K981_TOXGO 1-229 Xf | FAS1 domain-containing protein | A0A7J6KB94_TOXGO -9-699 Xg | DUF6832 domain-containing protein | A0A7J6KC93_TOXGO 12-486 Xh | RAP domain-containing protein | A0A7J6KAP7_TOXGO 1-632 Xi | RAP domain-containing protein | A0A7J6K2J1_TOXGO 1-445 Xj | RAP domain-containing protein | A0A7J6K4L1_TOXGO 1-955 Xk | RNA recognition motif-containing protein | A0A7J6KGH2_TOXGO 1-244 Xl Xv | RAP domain-containing protein | A0A7J6JZB1_TOXGO 1-645 Xm | Macro domain-containing protein | A0A7J6K515_TOXGO -104-506 Xn | AP2 domain transcription factor AP2VIIb-2 | A0A7J6K291_TOXGO 1-568 Xo | mL144 | Xp | Peptidyl-prolyl cis-trans isomerase | A0A7J6K9Z8_TOXGO 1-283 Xq | mL146 | A0A7J6K1X6_TOXGO 6-1117 Xr | RAP domain-containing protein | A0A7J6KAD2_TOXGO 1-713 Xs | mL149 | A0A7J6JXX4_TOXGO 1-493 Xt | mL148 | A0A7J6JV70_TOXGO 1-123 Xw | Transmembrane protein | A0A7J6KAS3_TOXGO 1-329 Xx | mL152 | A0A7J6K0Y0_TOXGO 1-300 Xy | mL153 | Q1JTA3_TOXGO 1-424 Xz | AP2 domain transcription factor AP2IV-1 | A0A7J6KEE5_TOXGO 1-425 Non-standard residues in 9i05 #1 --- FES — FE2/S2 (inorganic) cluster ZN — zinc ion > sequence chain #1/Xd Alignment identifier is 1/Xd > sequence chain #1/Xh Alignment identifier is 1/Xh > sequence chain #1/Xi Alignment identifier is 1/Xi > sequence chain #1/Xj Alignment identifier is 1/Xj > sequence chain #1/Xl#1/Xv Alignment identifier is 1 > sequence chain #1/Xr Alignment identifier is 1/Xr > sequence chain #1/Xr Destroying pre-existing alignment with identifier 1/Xr Alignment identifier is 1/Xr > sequence chain #1/Xr Alignment identifier is 1/Xr > sequence chain #1/Xl#1/Xv Alignment identifier is 1 > sequence chain #1/Xj Alignment identifier is 1/Xj > sequence chain #1/Xi Alignment identifier is 1/Xi > sequence chain #1/Xh Alignment identifier is 1/Xh > sequence chain #1/Xd Alignment identifier is 1/Xd > sequence chain #1/AI Alignment identifier is 1/AI > select > /AI:296-314,319-379,382-388,395-407,409-436,443-455,461-465,469-484,499-506,525-536,540-574,605-639 3842 atoms, 3861 bonds, 1 pseudobond, 236 residues, 2 models selected > show sel cartoons > hide sel cartoons > style sel stick Changed 3842 atom styles > style sel sphere Changed 3842 atom styles > show sel atoms > hide sel atoms > show sel atoms > hide #!1 models > show #!1 models > select add #1 323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models selected > select subtract #1 Nothing selected > select add #1 323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models selected > select subtract #1 Nothing selected > select /AI:295-639 5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected > select /AH:2-35 580 atoms, 583 bonds, 34 residues, 1 model selected > select /AH:2-35 580 atoms, 583 bonds, 34 residues, 1 model selected > sequence chain #1/AH Alignment identifier is 1/AH > sequence chain #1/AH Destroying pre-existing alignment with identifier 1/AH Alignment identifier is 1/AH > select /AI:295-639 5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected > set bgColor white > set bgColor black > style sel ball Changed 5401 atom styles > style sel ball Changed 5401 atom styles > style sel sphere Changed 5401 atom styles > style sel stick Changed 5401 atom styles > style sel stick Changed 5401 atom styles > style sel sphere Changed 5401 atom styles > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > hide sel atoms > hide sel surfaces > hide sel atoms > hide sel surfaces > select add #1.2 5401 atoms, 5458 bonds, 13 pseudobonds, 329 residues, 3 models selected > select add #1.1 5401 atoms, 5458 bonds, 1227 pseudobonds, 329 residues, 4 models selected > hide sel surfaces > hide sel cartoons > hide #!1 models > show #!1 models > select add #1 323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models selected > select subtract #1 Nothing selected > select add #1 323886 atoms, 332064 bonds, 1281 pseudobonds, 17930 residues, 4 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > show sel atoms > hide sel atoms > select /AI:295-639 5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected > select #AI Expected an objects specifier or a keyword > select AI Expected an objects specifier or a keyword > select #1/AI 5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected > cartoon (#!1 & sel) > color (#!1 & sel) red > select clear > select /AI:551 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 314 atoms, 313 bonds, 21 residues, 1 model selected > select up 4564 atoms, 4611 bonds, 279 residues, 1 model selected > select down 314 atoms, 313 bonds, 21 residues, 1 model selected > select down 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 314 atoms, 313 bonds, 21 residues, 1 model selected > select up 4564 atoms, 4611 bonds, 279 residues, 1 model selected > select up 5401 atoms, 5458 bonds, 329 residues, 1 model selected > color sel green > show sel atoms > hide sel atoms > select /AI:14 Nothing selected > select /AI:406 10 atoms, 9 bonds, 1 residue, 1 model selected > select /AI:cys 11 atoms, 10 bonds, 1 residue, 1 model selected > select /AI:lys 462 atoms, 442 bonds, 21 residues, 1 model selected > select /AI:K Nothing selected > select /AI:K Nothing selected > select /AI 5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected > name frozen AI sel > select clear > select AI 5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected > show #1 > show #1 cartoons > hide sel atoms > hide sel cartoons > hide sel surfaces > show #1 cartoons > ~hbonds > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 5401 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > show #1 cartoons > hide sel surfaces > hide sel cartoons > show sel cartoons > hide sel atoms > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel ball Changed 5401 atom styles > style sel ball Changed 5401 atom styles > style sel cartoons Expected a keyword > style sel off Expected a keyword > style sel stick Changed 5401 atom styles > style #1 stick Changed 323886 atom styles > hide sel atoms > style #1 cartoons Expected a keyword > hide sel atoms > hide #1 > color #1 grey > select clear > name frozen AI sel Nothing is selected by specifier > select AI 5401 atoms, 5458 bonds, 1 pseudobond, 329 residues, 2 models selected > color (#!1 & sel) red > select clear > set bgColor white > lighting simple > lighting soft > lighting full > show surfaces > lighting simple > lighting soft > lighting full > open 9hqv fromDatabase pdb format mmcif Summary of feedback from opening 9hqv fetched from pdb --- warnings | Atom H is not in the residue template for PRO /Ba:87 Atom H1 is not in the residue template for UNK /Ua:1 Atom H1 is not in the residue template for UNK /Uc:1 Atom H1 is not in the residue template for UNK /Ud:1 Atom H3 is not in the residue template for UNK /Ui:1 Atom H1 is not in the residue template for UNK /Uj:1 Atom H3 is not in the residue template for UNK /Uk:1 Atom H1 is not in the residue template for UNK /Uo:1 Atom H1 is not in the residue template for UNK /Up:1 Too many hydrogens missing from residue template(s) to warn about notes | Fetching compressed mmCIF 9hqv from http://files.rcsb.org/download/9hqv.cif Fetching CCD ATP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 9hqv title: Cryo-EM structure of the small subunit of the mitochondrial ribosome from Toxoplasma gondii [more info...] Chain information for 9hqv #2 --- Chain | Description | UniProt BA | Enoyl-CoA hydratase/isomerase family protein | A0A7J6KGS2_TOXGO 1-716 BB | mS75 | BC | Pentatricopeptide repeat domain-containing protein | A0A7J6KDF6_TOXGO 1-686 BD | mS92 | A0A7J6KCE0_TOXGO 1-147 Ba | Ribosomal protein, uS2m | A0A7J6K4L0_TOXGO 1-190 Bb | Putative 30S ribosomal protein S5 | A0A7J6KBH4_TOXGO 34-1141 Bc | Putative mitochondrial ribosomal protein s6-2 | A0A7J6K9W0_TOXGO 1-163 Bd | Putative ribosomal protein S8 | A0A7J6K132_TOXGO 1-129 Be | Putative ribosomal protein S9 | A0A7J6KFS1_TOXGO 1-530 Bf | uS10m | A0A7J6K2E1_TOXGO 1-243 Bg | Putative ribosomal protein S11 | A0A7J6K2Q1_TOXGO 1-393 Bh | Putative 30S ribosomal protein S12 | A0A7J6JTW0_TOXGO 1-594 Bi | us13m | A0A7J6KC71_TOXGO -6-103 Bj | Putative ribosomal protein S14 | A0A7J6JW76_TOXGO 1-112 Bk | Putative 30S ribosomal protein S15 | A0A7J6JZR0_TOXGO 1-395 Bl | Putative 30S ribosomal protein S16 | A0A7J6KCY1_TOXGO 1-167 Bm | Putative ribosomal protein S17 | A0A125YU94_TOXGG 1-116 Bn | Putative ribosomal protein S18 | S7VTU6_TOXGG 1-738 Bo | Ribosomal protein, bS21m | S8G0I7_TOXGM 1-243 Bp | mS23 | A0A7J6K2Y2_TOXGO 1-377 Bq | Mitochondrial ribosomal protein, mS26 | A0A086KM95_TOXGO 1-447 Br | Small ribosomal subunit protein mS29 | A0A7J6JWV4_TOXGO 1-545 Bs | DNA double-strand break repair rad50 ATPase | A0A7J6K0I6_TOXGO 1-616 Bt | mS34 | A0A7J6JYF4_TOXGO 1-303 Bu | Small ribosomal subunit protein mS35 mitochondrial conserved domain-containing protein | A0A7J6K5S5_TOXGO 2-584 Bv | CHCH domain-containing protein | A0A7J6JX47_TOXGO 1-138 Bx | Mitochondrial mRNA-processing protein COX24 C-terminal domain-containing protein | A0A0F7UNZ9_TOXGV -190-76 By | Homeodomain-like containing protein | A0A7J6KAD0_TOXGO -323-273 Bz | mS45 | A0A7J6JZ68_TOXGO 1-531 SA | SSU-1 | SB | SSU-2 | SC | SSU-3 | SD | SSU-4 | SE | SSU-5 | SF | SSU-6 | SG | SSU-7 | SH | SSU-8 | SI | SSU-9 | SJ | SSU-10 | SK | SSU-11 | SL | SSU-12 | SM | SSU-13 | SN | SSU-14 | SO | SSU-15 | SP | SSU-16 | SQ | SSU-17 | SR | SSU-18 | SS | SSU-19 | ST | SSU-20 | SU | SSU-21 | TP | tRNA E-site | UC | Chain UC | Ua | UNK1 | Ub | UNK2 | Uc | UNK3 | Ud | UNK4 | Uh | Chain Uh | Ui Uk | Unknown peptide | Uj | Chain Uj | Ul | GLY-ARG-SER-LYS-VAL-LEU-ILE-ARG-ARG-LEU-LYS-GLU-ARG-ALA-LYS-LYS-GLU-ALA-GLU-LYS-LYS-ALA | Um | ARG-ALA-GLU-LEU-VAL-ALA-ALA-GLN-VAL-ARG-GLU-LYS-LEU-ALA-ILE-LYS-MET-ALA-ASN-ALA-LEU-ALA | Un | Chain Un | Uo | chain Uo | Up | chain Up | Uq | chain Uq | Ya | mS117 | S7V2J1_TOXGG 1-551 Yb | ATP-dependent Clp protease proteolytic subunit,related protein | A0A7J6K1B3_TOXGO 0-1159 Yc | mS119 | A0A7J6KFI1_TOXGO 0-267 Yd | mS120 | A0A7J6K8Y5_TOXGO 1-680 Ye | mS121 | A0A7J6JZ58_TOXGO 1-314 Yf | Macro domain-containing protein | A0A7J6K475_TOXGO 1-698 Yg | Thioredoxin domain-containing protein | A0A7J6K257_TOXGO -17-1038 Yh | mS124 | Yi | mS125 | A0A7J6JYP0_TOXGO 1-931 Yj | DnaJ domain-containing protein | A0A7J6KC34_TOXGO -168-64 Yk | RAP domain-containing protein | A0A7J6KGV4_TOXGO 1-1553 Yl | mS128 | A0A7J6KEX1_TOXGO 1-316 Ym | RAP domain-containing protein | A0A7J6K7K5_TOXGO 1-801 Yn | AP2 domain transcription factor AP2IX-6 | A0A7J6KDC3_TOXGO 1-432 Yo | mS131 | A0A7J6KFW2_TOXGO 1-421 Yp | mS132 | A0A7J6K2N1_TOXGO 1-180 Yq | mS133 | B9PYD6_TOXGO -2-302 Yr | Acylphosphatase-like domain-containing protein | A0A125YXT0_TOXGG 1-235 Ys | mS135 | A0A7J6K0G8_TOXGO 1-181 Yt | mS136 | A0A7J6K0Z5_TOXGO 1-475 Yu | mS137 | Yv | mS138 | A0A7J6K328_TOXGO 1-419 Non-standard residues in 9hqv #2 --- ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide #!1 models > show #!1 models > hide #1 > hide #1 surfaces > hide #1 cartoons > select add #1.4 3132 atoms, 188 residues, 1 model selected > select subtract #1.4 1 model selected > ui mousemode right ""translate selected models"" > unhide #1 cartoons Unknown command: unhide #1 cartoons > show #1 cartoons > color #1/ RE green > lighting simple > hide #!2 models > ui mousemode right ""translate selected models"" > select clear > color #1/ Xh cyan > color #1/ RA pink > color #1/ RG cyan > color #1/ Xh grey > ui mousemode right ""move picked models"" > view matrix models #1,1,0,0,6.3129,0,1,0,-6.2262,0,0,1,-0.79302 > ui mousemode right ""translate selected models"" > color #1/ RA rose Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/ RA violet > lighting simple > lighting soft > lighting full > lighting simple > color #1/ Aq Blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/ Aq blue > save /Users/dhanyshanmugam/Desktop/image1.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image2.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image3.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image4.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image5.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image6.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image7.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image8.png supersample 3 > show #!2 models > save /Users/dhanyshanmugam/Desktop/image9.png supersample 3 > hide #!2 models > color #1/ AG yellow > color #1/ AG grey > color #1/ RB yellow > color #1/ Rc brown > color #1/ Rd brown > color #1/ Rc grey > color #1/ Rd grey > color #1/ Rf brown > color #1/ Rf grey > color #1/ RC brown > ui tool show ""Selection Inspector"" > color #1/ RC grey > color #1/ RD brown > color #1/ RD grey > color #1/ RF brown > color #1/ RF grey > color #1/ RI brown > color #1/ RI grey > color #1/ RJ brown > color #1/ RJ grey > color #1/ RK brown > color #1/ RK grey > color #1/ RL brown > color #1/ RL grey > color #1/ RM brown > color #1/ RM grey > color #1/ RN brown > color #1/ RN grey > color #1/ RO brown > color #1/ RO grey > color #1/ RP brown > color #1/ RP grey > color #1/ RQ brown > color #1/ RQ grey > color #1/ RR brown > color #1/ RS brown > color #1/ RS grey > color #1/ RT brown > color #1/ RT grey > color #1/ RU brown > color #1/ RU grey > color #1/ RV brown > color #1/ RV grey > color #1/ RW brown > color #1/ RW grey > color #1/ RX brown > color #1/ RX grey > color #1/ RY brown > select ~sel & ##selected Nothing selected > color #1/ RY grey > color #1/ RZ brown > color #1/ RZ grey > color #1/ Ra brown > color #1/ Ra grey > color #1/ Rb brown > color #1/ Rb grey > color #1/ Rc brown > color #1/ Rc grey > color #1/ Rd brown > color #1/ Rd grey > color #1/ Rf brown > color #1/ Rf grey > color #1/ Rg brown > color #1/ Rg grey > color #1/ Rh brown > color #1/ Rh grey > color #1/ Ri brown > color #1/ Ri grey > save /Users/dhanyshanmugam/Desktop/image10.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image11.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image12.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image13.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image14.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image15.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image16.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image17.png supersample 3 > color #1/ Rb brown > color #1/ Rb grey > color #1/ Rd brown > color #1/ Rd grey > color #1/ Rh brown > color #1/ Rh grey > color #1/ Xb brown > color #1/ Xb grey > color #1/ Xd brown > show #!2 models > hide #!2 models > color #1/ Xd grey > color #1/ Xh brown > color #1/ Xh grey > color #1/ Xi brown > show #!2 models > hide #!2 models > color #1/ Xi grey > color #1/ Xj brown > color #1/ Xj grey > color #1/ Xk brown > color #1/ Xk yellow > color #1/ Xk grey > color #1/ XI yellow > color #1/ XI goldenrod > color #1/ XI gold > color #1/ XI grey > color #1/ X1 yellow > color #1/ X1 grey > color #1/ Xv brown > color #1/ Xv grey > color #1/ Xr brown > show #!2 models > hide #!2 models > color #1/ Xr goldenrod > color #1/ Xd goldenrod > color #1/ Xh goldenrod > color #1/ Xi goldenrod > color #1/ Xj goldenrod > color #1/ X1 goldenrod > color #1/ Xv goldenrod > color #1/ Xr goldenrod > color #1/ Xr blue > color #1/ Xr goldenrod > color #1/ Xr blue > color #1/ Xr goldenrod > color #1/ Xv blue > color #1/ Xv goldenrod > color #1/ Xj blue > color #1/ Xi blue > color #1/ Xh blue > color #1/ Xd blue > color #1/ Xv blue > color #1/ Xv goldenrod > color #1/ Xd goldenrod > color #1/ Xh goldenrod > color #1/ Xi goldenrod > color #1/ Xj goldenrod > color #1/ Xv goldenrod > color #1/ Xk blue > color #1/ Xb blue > color #1/ Xb grey > color #1/ Xk grey > save /Users/dhanyshanmugam/Desktop/image18.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image19.png supersample 3 > save /Users/dhanyshanmugam/Desktop/image20.png supersample 3 > show #!2 models > style stick Changed 570134 atom styles > style ball Changed 570134 atom styles > style stick Changed 570134 atom styles > style sphere Changed 570134 atom styles > style sphere Changed 570134 atom styles > style ball Changed 570134 atom styles > color bychain > nucleotides atoms > style nucleic stick Changed 98216 atom styles > show surfaces > hide surfaces > show surfaces > hide #!1 models > select add #2 246248 atoms, 251434 bonds, 773 pseudobonds, 14185 residues, 4 models selected > color #2 grey > select subtract #2 88 models selected > show #!1 models > select add #1 323886 atoms, 332064 bonds, 67 pseudobonds, 17930 residues, 3 models selected > color #1 grey > select subtract #1 108 models selected > lighting simple > lighting soft > save /Users/dhanyshanmugam/Desktop/image21.png supersample 3 > color #1 pink > save /Users/dhanyshanmugam/Desktop/image22.png supersample 3 > color #1 grey > color #2 pink > save /Users/dhanyshanmugam/Desktop/image23.png supersample 3 > color #2 skyblue > color #1/ AI red > save /Users/dhanyshanmugam/Desktop/image24.png supersample 3 > color #1/ AI grey > save /Users/dhanyshanmugam/Desktop/image25.png supersample 3 > color #1/ AI red > color #1/ RE green > color #1/ RE grey > color #1/ Aq blue > color #1/ Xd goldenrod > color #1/ Xh goldenrod > color #1/ Xi goldenrod > color #1/ Xj goldenrod > color #1/ Xv goldenrod > color #1/ Xr goldenrod > color #1/ Xr blue > color #1/ Xr goldenrod > save /Users/dhanyshanmugam/Desktop/image26.png supersample 3 > select add #1.89 7539 atoms, 492 residues, 1 model selected > view #1 clip false > sequence chain #1/Xd Alignment identifier is 1/Xd > select subtract #1.89 1 model selected > select add #1.93 6863 atoms, 421 residues, 1 model selected > sequence chain #1/Xh Alignment identifier is 1/Xh > select subtract #1.93 1 model selected > select add #1.94 7329 atoms, 444 residues, 1 model selected > sequence chain #1/Xi Alignment identifier is 1/Xi > select subtract #1.94 1 model selected > select add #1.95 9609 atoms, 585 residues, 1 model selected > sequence chain #1/Xj Alignment identifier is 1/Xj > select subtract #1.95 1 model selected > select add #1.103 7423 atoms, 451 residues, 1 model selected > sequence chain #1/Xr Alignment identifier is 1/Xr > select subtract #1.103 1 model selected > select add #1.106 6386 atoms, 394 residues, 1 model selected > sequence chain #1/Xv Alignment identifier is 1/Xv > select subtract #1.106 1 model selected > color #1/ Xl goldenrod > color #1/ Xl blue > color #1/ Xv blue > color #1/ Xv pink > color #1/ Xl pink > color #1/ Xr pink > color #1/ Xr goldenrod > hide #!2 models > show #!2 models > hide surfaces > sequence chain #1/Aa Alignment identifier is 1/Aa > sequence chain #1/Ab Alignment identifier is 1/Ab > sequence chain #1/Ac Alignment identifier is 1/Ac > sequence chain #1/Ad Alignment identifier is 1/Ad > sequence chain #1/Ae Alignment identifier is 1/Ae > sequence chain #1/Af Alignment identifier is 1/Af > sequence chain #1/Ag Alignment identifier is 1/Ag > sequence chain #1/Ah Alignment identifier is 1/Ah > sequence chain #1/Ai Alignment identifier is 1/Ai > sequence chain #1/Aj Alignment identifier is 1/Aj > sequence chain #1/Ak Alignment identifier is 1/Ak > sequence chain #1/Al Alignment identifier is 1/Al > sequence chain #1/Am Alignment identifier is 1/Am > sequence chain #1/An Alignment identifier is 1/An > sequence chain #1/Ao Alignment identifier is 1/Ao > sequence chain #1/Ap Alignment identifier is 1/Ap > sequence chain #1/Aq Alignment identifier is 1/Aq > sequence chain #1/Ar Alignment identifier is 1/Ar > sequence chain #1/As Alignment identifier is 1/As > sequence chain #1/At Alignment identifier is 1/At > sequence chain #1/Au Alignment identifier is 1/Au > sequence chain #1/Av Alignment identifier is 1/Av > sequence chain #1/Aw Alignment identifier is 1/Aw > sequence chain #1/Ax Alignment identifier is 1/Ax > sequence chain #1/Ay Alignment identifier is 1/Ay > sequence chain #1/Az Alignment identifier is 1/Az > sequence chain #1/AA Alignment identifier is 1/AA > sequence chain #1/AB Alignment identifier is 1/AB > sequence chain #1/AC Alignment identifier is 1/AC > sequence chain #1/AD Alignment identifier is 1/AD > sequence chain #1/AE Alignment identifier is 1/AE > sequence chain #1/AF Alignment identifier is 1/AF > sequence chain #1/AG Alignment identifier is 1/AG > sequence chain #1/AH Alignment identifier is 1/AH > sequence chain #1/AI Alignment identifier is 1/AI > sequence chain #1/Xa Alignment identifier is 1/Xa > sequence chain #1/Xb Alignment identifier is 1/Xb > sequence chain #1/Xc Alignment identifier is 1/Xc > sequence chain #1/Xd Alignment identifier is 1/Xd > sequence chain #1/Xe Alignment identifier is 1/Xe > sequence chain #1/Xf Alignment identifier is 1/Xf > sequence chain #1/Xg Alignment identifier is 1/Xg > sequence chain #1/Xh Alignment identifier is 1/Xh > sequence chain #1/Xi Alignment identifier is 1/Xi > sequence chain #1/Xj Alignment identifier is 1/Xj > sequence chain #1/Xk Alignment identifier is 1/Xk > sequence chain #1/Xl,Xv Alignment identifier is 1 > sequence chain #1/Xm Alignment identifier is 1/Xm > sequence chain #1/Xn Alignment identifier is 1/Xn > sequence chain #1/Xo Alignment identifier is 1/Xo > sequence chain #1/Xp Alignment identifier is 1/Xp > sequence chain #1/Xq Alignment identifier is 1/Xq > sequence chain #1/Xr Alignment identifier is 1/Xr > sequence chain #1/Xs Alignment identifier is 1/Xs > sequence chain #1/Xt Alignment identifier is 1/Xt > sequence chain #1/Xw Alignment identifier is 1/Xw > sequence chain #1/Xx Alignment identifier is 1/Xx > sequence chain #1/Xy Alignment identifier is 1/Xy > sequence chain #1/Xz Alignment identifier is 1/Xz > sequence chain #1/XA Alignment identifier is 1/XA > sequence chain #1/XB Alignment identifier is 1/XB > sequence chain #1/XC Alignment identifier is 1/XC > sequence chain #1/XD Alignment identifier is 1/XD > sequence chain #1/XE Alignment identifier is 1/XE > sequence chain #1/XF Alignment identifier is 1/XF > sequence chain #1/XG Alignment identifier is 1/XG > sequence chain #1/XH Alignment identifier is 1/XH > sequence chain #1/XI Alignment identifier is 1/XI > sequence chain #1/XJ Alignment identifier is 1/XJ > sequence chain #1/Ua Alignment identifier is 1/Ua > sequence chain #1/Ub Alignment identifier is 1/Ub > sequence chain #1/Uc Alignment identifier is 1/Uc > sequence chain #1/Ud Alignment identifier is 1/Ud > sequence chain #1/Ue Alignment identifier is 1/Ue > sequence chain #1/Uf Alignment identifier is 1/Uf > sequence chain #1/RA Alignment identifier is 1/RA > sequence chain #1/RB Alignment identifier is 1/RB > sequence chain #1/RC Alignment identifier is 1/RC > sequence chain #1/RD Alignment identifier is 1/RD > sequence chain #1/RE Alignment identifier is 1/RE > sequence chain #1/RF Alignment identifier is 1/RF > sequence chain #1/RG Alignment identifier is 1/RG > sequence chain #1/RI Alignment identifier is 1/RI > sequence chain #1/RJ Alignment identifier is 1/RJ > sequence chain #1/RK Alignment identifier is 1/RK > sequence chain #1/RL Alignment identifier is 1/RL > sequence chain #1/RM Alignment identifier is 1/RM > sequence chain #1/RN Alignment identifier is 1/RN > sequence chain #1/RO Alignment identifier is 1/RO > sequence chain #1/RP Alignment identifier is 1/RP > sequence chain #1/RQ Alignment identifier is 1/RQ > sequence chain #1/RS Alignment identifier is 1/RS > sequence chain #1/RT Alignment identifier is 1/RT > sequence chain #1/RU Alignment identifier is 1/RU > sequence chain #1/RV Alignment identifier is 1/RV > sequence chain #1/RW Alignment identifier is 1/RW > sequence chain #1/RX Alignment identifier is 1/RX > sequence chain #1/RY Alignment identifier is 1/RY > sequence chain #1/RZ Alignment identifier is 1/RZ > sequence chain #1/Ra Alignment identifier is 1/Ra > sequence chain #1/Rb Alignment identifier is 1/Rb > sequence chain #1/Rc Alignment identifier is 1/Rc > sequence chain #1/Rd Alignment identifier is 1/Rd > sequence chain #1/Rf Alignment identifier is 1/Rf > sequence chain #1/Rg Alignment identifier is 1/Rg > sequence chain #1/Rh Alignment identifier is 1/Rh > sequence chain #1/Ri Alignment identifier is 1/Ri > sequence chain #2/BA Alignment identifier is 2/BA > sequence chain #2/BB Alignment identifier is 2/BB > sequence chain #2/BC Alignment identifier is 2/BC > sequence chain #2/BD Alignment identifier is 2/BD > sequence chain #2/Ba Alignment identifier is 2/Ba > sequence chain #2/Bb Alignment identifier is 2/Bb > sequence chain #2/Bc Alignment identifier is 2/Bc > sequence chain #2/Bd Alignment identifier is 2/Bd > sequence chain #2/Be Alignment identifier is 2/Be > sequence chain #2/Bf Alignment identifier is 2/Bf > sequence chain #2/Bg Alignment identifier is 2/Bg > sequence chain #2/Bh Alignment identifier is 2/Bh > sequence chain #2/Bi Alignment identifier is 2/Bi > sequence chain #2/Bj Alignment identifier is 2/Bj > sequence chain #2/Bk Alignment identifier is 2/Bk > sequence chain #2/Bl Alignment identifier is 2/Bl > sequence chain #2/Bm Alignment identifier is 2/Bm > sequence chain #2/Bn Alignment identifier is 2/Bn > sequence chain #2/Bo Alignment identifier is 2/Bo > sequence chain #2/Bp Alignment identifier is 2/Bp > sequence chain #2/Bq Alignment identifier is 2/Bq > sequence chain #2/Br Alignment identifier is 2/Br > sequence chain #2/Bs Alignment identifier is 2/Bs > sequence chain #2/Bt Alignment identifier is 2/Bt > sequence chain #2/Bu Alignment identifier is 2/Bu > sequence chain #2/Bv Alignment identifier is 2/Bv > sequence chain #2/Bx Alignment identifier is 2/Bx > sequence chain #2/By Alignment identifier is 2/By > sequence chain #2/Bz Alignment identifier is 2/Bz > sequence chain #2/Ua Alignment identifier is 2/Ua > sequence chain #2/Ub Alignment identifier is 2/Ub > sequence chain #2/Uc Alignment identifier is 2/Uc > sequence chain #2/Ud Alignment identifier is 2/Ud > sequence chain #2/Uh Alignment identifier is 2/Uh > sequence chain #2/Ui,Uk Alignment identifier is 2 > sequence chain #2/Uj Alignment identifier is 2/Uj > sequence chain #2/Ul Alignment identifier is 2/Ul > sequence chain #2/Um Alignment identifier is 2/Um > sequence chain #2/Un Alignment identifier is 2/Un > sequence chain #2/Uo Alignment identifier is 2/Uo > sequence chain #2/Up Alignment identifier is 2/Up > sequence chain #2/Uq Alignment identifier is 2/Uq > sequence chain #2/Ya Alignment identifier is 2/Ya > sequence chain #2/Yb Alignment identifier is 2/Yb > sequence chain #2/Yc Alignment identifier is 2/Yc > sequence chain #2/Yd Alignment identifier is 2/Yd > sequence chain #2/Ye Alignment identifier is 2/Ye > sequence chain #2/Yf Alignment identifier is 2/Yf > sequence chain #2/Yg Alignment identifier is 2/Yg > sequence chain #2/Yh Alignment identifier is 2/Yh > sequence chain #2/Yi Alignment identifier is 2/Yi > sequence chain #2/Yj Alignment identifier is 2/Yj > sequence chain #2/Yk Alignment identifier is 2/Yk > sequence chain #2/Yl Alignment identifier is 2/Yl > sequence chain #2/Ym Alignment identifier is 2/Ym > sequence chain #2/Yn Alignment identifier is 2/Yn > sequence chain #2/Yo Alignment identifier is 2/Yo > sequence chain #2/Yp Alignment identifier is 2/Yp > sequence chain #2/Yr Alignment identifier is 2/Yr > sequence chain #2/Ys Alignment identifier is 2/Ys > sequence chain #2/Yt Alignment identifier is 2/Yt > sequence chain #2/Yu Alignment identifier is 2/Yu > sequence chain #2/Yq Alignment identifier is 2/Yq > sequence chain #2/SA Alignment identifier is 2/SA > sequence chain #2/SB Alignment identifier is 2/SB > sequence chain #2/SC Alignment identifier is 2/SC > sequence chain #2/SD Alignment identifier is 2/SD > sequence chain #2/SE Alignment identifier is 2/SE > sequence chain #2/SF Alignment identifier is 2/SF > sequence chain #2/SG Alignment identifier is 2/SG > sequence chain #2/SH Alignment identifier is 2/SH > sequence chain #2/SI Alignment identifier is 2/SI > sequence chain #2/SJ Alignment identifier is 2/SJ > sequence chain #2/SK Alignment identifier is 2/SK > sequence chain #2/SL Alignment identifier is 2/SL > sequence chain #2/SM Alignment identifier is 2/SM > sequence chain #2/SN Alignment identifier is 2/SN > sequence chain #2/SO Alignment identifier is 2/SO > sequence chain #2/SP Alignment identifier is 2/SP > sequence chain #2/SQ Alignment identifier is 2/SQ > sequence chain #2/SR Alignment identifier is 2/SR > sequence chain #2/SS Alignment identifier is 2/SS > sequence chain #2/ST Alignment identifier is 2/ST > sequence chain #2/SU Alignment identifier is 2/SU > sequence chain #2/TP Alignment identifier is 2/TP > sequence chain #2/UC Alignment identifier is 2/UC > sequence chain #2/Yv Alignment identifier is 2/Yv ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: MRX43HN/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 12 days, 14 hours, 35 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 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit can't reproduce Eric Pettersen all ChimeraX