id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19225 Crash repainting widget chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x000000020a6c20c0 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.connect_structure._cs, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 49) 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All rights reserved. How to cite UCSF ChimeraX > open /Users/c.lewis.2/job036.cif format mmcif Summary of feedback from opening /Users/c.lewis.2/job036.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for job036.cif #1 --- Chain | Description A0 | No description available A1 A2 A4 A5 A6 A8 A9 Ab Ac Ad Ae Af Ag Ai Aj Ak Al Am An Ao Ap As Au Ay Az | No description available A3 A7 Aaa | No description available Aa Aa4 Aa6 Aa8 Aab Aad Aae Aaf Aag Aai Aaj Aak Aam Aao Aap Aar Ah Ax | No description available Aa0 | No description available Aa1 Aa2 Aax Aay Aaz Ac2 Acm Acp Acq Act Acx Acz | No description available Aa3 Adc Add Adh Adi | No description available Aa5 Aal Aan Aaq Aas | No description available Aa7 Aa9 Aba | No description available Aac | No description available Aah | No description available Aat Ab0 Abd Abe Abh Abi Abj Abn Abr Abx Acg | No description available Aau Aav Ab1 Ab2 Ab3 Ab4 Ab5 Abc Abf Abg Abk Abl Abm Abo Abp Abq Abs Abt Abu Abv Abw Aby Abz Acf Aci Acj Acl | No description available Aaw | No description available Ab6 Ac0 Ac1 Ac6 Ac7 Ac8 Acr Acs Acu Acw | No description available Ab7 Ab8 Ab9 Ac3 Acn Aco Acv Acy | No description available Abb | No description available Ac4 Ac5 Ad1 Ady | No description available Ac9 | No description available Aca Acb Adl Adw Adx | No description available Acc Acd Ad2 Ad3 Ad4 Ad5 Adf Adg Adq Adr Adu | No description available Ace | No description available Ach | No description available Ack | No description available Ad0 Adm Adt Adv | No description available Ad6 | No description available Ad7 | No description available Ada | No description available Adb Ads | No description available Ade | No description available Adj | No description available Adk Adn Adp | No description available Ado Ar Aw | No description available Adz | No description available Aq | No description available At | No description available Av | No description available B0 | No description available B1 | No description available B2 | No description available B3 | No description available B4 | No description available B5 | No description available B6 | No description available B7 | No description available B8 | No description available B9 | No description available Ba | No description available Ba0 | No description available Ba1 | No description available Ba2 | No description available Ba3 | No description available Ba4 | No description available Ba5 | No description available Ba6 | No description available Ba7 | No description available Ba8 | No description available Ba9 | No description available Baa | No description available Bab | No description available Bac | No description available Bad | No description available Bae | No description available Baf | No description available Bag | No description available Bah | No description available Bai | No description available Baj | No description available Bak | No description available Bal | No description available Bam | No description available Ban | No description available Bao | No description available Bap | No description available Baq | No description available Bar | No description available Bas | No description available Bat | No description available Bau | No description available Bav | No description available Baw | No description available Bax | No description available Bay | No description available Baz | No description available Bb | No description available Bb0 | No description available Bb1 | No description available Bb2 | No description available Bb3 | No description available Bb4 | No description available Bb5 | No description available Bb6 | No description available Bb7 | No description available Bb8 | No description available Bb9 | No description available Bba | No description available Bbb | No description available Bbc | No description available Bbd | No description available Bbe | No description available Bbf | No description available Bbg | No description available Bbh | No description available Bbi | No description available Bbj | No description available Bbk | No description available Bbl | No description available Bbm | No description available Bbn | No description available Bbo | No description available Bbp | No description available Bbq | No description available Bbr | No description available Bbs | No description available Bbt | No description available Bbu | No description available Bbv | No description available Bbw | No description available Bbx | No description available Bby | No description available Bbz | No description available Bc | No description available Bc0 | No description available Bc1 | No description available Bc2 | No description available Bc3 | No description available Bc4 | No description available Bc5 | No description available Bc6 | No description available Bc7 | No description available Bc8 Biv | No description available Bc9 | No description available Bca | No description available Bcb | No description available Bcc | No description available Bcd | No description available Bce | No description available Bcf | No description available Bcg | No description available Bch | No description available Bci Bd4 | No description available Bcj | No description available Bck | No description available Bcl | No description available Bcm | No description available Bcn | No description available Bco | No description available Bcp | No description available Bcq | No description available Bcr | No description available Bcs | No description available Bct | No description available Bcu | No description available Bcv | No description available Bcw | No description available Bcx | No description available Bcy | No description available Bcz | No description available Bd | No description available Bd0 | No description available Bd1 | No description available Bd2 | No description available Bd3 | No description available Bd5 | No description available Bd6 | No description available Bd7 | No description available Bd8 | No description available Bd9 | No description available Bda | No description available Bdb | No description available Bdc | No description available Bdd | No description available Bde | No description available Bdf | No description available Bdg | No description available Bdh | No description available Bdi | No description available Bdj | No description available Bdk | No description available Bdl | No description available Bdm | No description available Bdn | No description available Bdo | No description available Bdp | No description available Bdq | No description available Bdr | No description available Bds | No description available Bdt | No description available Bdu | No description available Bdv | No description available Bdw | No description available Bdx | No description available Bdy | No description available Bdz | No description available Be | No description available Be0 | No description available Be1 | No description available Be2 | No description available Be3 | No description available Be4 | No description available Be5 | No description available Be6 | No description available Be7 | No description available Be8 | No description available Be9 | No description available Bea | No description available Beb | No description available Bec | No description available Bed | No description available Bee | No description available Bef | No description available Beg | No description available Beh | No description available Bei | No description available Bej | No description available Bek | No description available Bel | No description available Bem | No description available Ben | No description available Beo | No description available Bep | No description available Beq | No description available Ber | No description available Bes | No description available Bet | No description available Beu | No description available Bev | No description available Bew | No description available Bex | No description available Bey | No description available Bez | No description available Bf | No description available Bf0 | No description available Bf1 | No description available Bf2 | No description available Bf3 | No description available Bf4 Bg7 Bhi | No description available Bf6 | No description available Bf7 | No description available Bf8 | No description available Bfa | No description available Bfb | No description available Bfc | No description available Bfd | No description available Bfe | No description available Bff | No description available Bfg | No description available Bfh | No description available Bfi Bfw | No description available Bfj | No description available Bfk | No description available Bfl | No description available Bfm | No description available Bfn | No description available Bfo | No description available Bfp | No description available Bfr | No description available Bfs | No description available Bft | No description available Bfu | No description available Bfv | No description available Bfx | No description available Bfy | No description available Bfz | No description available Bg | No description available Bg0 | No description available Bg1 | No description available Bg2 | No description available Bg3 | No description available Bg4 | No description available Bg5 | No description available Bg6 | No description available Bg8 | No description available Bg9 | No description available Bga | No description available Bgb | No description available Bgc | No description available Bgd | No description available Bge | No description available Bgf | No description available Bgg | No description available Bgh | No description available Bgi | No description available Bgj | No description available Bgk Biz | No description available Bgl | No description available Bgm | No description available Bgn | No description available Bgo | No description available Bgp | No description available Bgq | No description available Bgr | No description available Bgs | No description available Bgt | No description available Bgu | No description available Bgv | No description available Bgw | No description available Bgx | No description available Bgy | No description available Bgz Bht | No description available Bh | No description available Bh0 | No description available Bh1 | No description available Bh2 | No description available Bh3 | No description available Bh4 | No description available Bh5 | No description available Bh6 | No description available Bh7 | No description available Bh8 | No description available Bh9 Bhw Bie | No description available Bha | No description available Bhb | No description available Bhc | No description available Bhd | No description available Bhe | No description available Bhf | No description available Bhg | No description available Bhh | No description available Bhj | No description available Bhk | No description available Bhl | No description available Bhm | No description available Bhn | No description available Bho Bhv | No description available Bhp | No description available Bhq | No description available Bhr | No description available Bhs | No description available Bhu | No description available Bhx | No description available Bhy | No description available Bhz | No description available Bi | No description available Bi0 | No description available Bi1 | No description available Bi2 | No description available Bi3 | No description available Bi4 | No description available Bi5 | No description available Bi6 | No description available Bi7 | No description available Bi8 | No description available Bi9 Bja Bjb Bje Bjf Bji Bjj | No description available Bia | No description available Bib | No description available Bic | No description available Bid | No description available Bif | No description available Big | No description available Bih | No description available Bii | No description available Bij | No description available Bik Bin | No description available Bil | No description available Bim | No description available Bio | No description available Bip | No description available Biq | No description available Bir | No description available Bis | No description available Bit | No description available Biu | No description available Biw | No description available Bix | No description available Biy | No description available Bj | No description available Bjc | No description available Bjd | No description available Bjg | No description available Bjh | No description available Bjk | No description available Bjl | No description available Bjm | No description available Bk | No description available Bl | No description available Bm | No description available Bn | No description available Bo | No description available Bp | No description available Bq | No description available Br | No description available Bs | No description available Bt | No description available Bu | No description available Bv | No description available Bw | No description available Bx | No description available By | No description available Bz | No description available Cannot find consistent set of bond orders for ring system containing atom CG in residue PHE /Bcf:487 Cannot find consistent set of bond orders for ring system containing atom CD2 in residue TRP /Be:384 > show surfaces Alignment identifier is 1 Computing secondary structure Alignment identifier is 1/Ba Alignment identifier is 2 Alignment identifier is 1/Bb Alignment identifier is 1/Aq Alignment identifier is 3 Alignment identifier is 1/At Alignment identifier is 1/Av Alignment identifier is 1/Bc Alignment identifier is 1/Bd Alignment identifier is 1/Be Alignment identifier is 1/Bf Alignment identifier is 1/Bg Alignment identifier is 1/Bh Alignment identifier is 1/Bi Alignment identifier is 1/Bj Alignment identifier is 1/Bk Alignment identifier is 1/Bl Alignment identifier is 1/Bm Alignment identifier is 1/Bn Alignment identifier is 1/Bo Alignment identifier is 1/Bp Alignment identifier is 1/Bq Alignment identifier is 1/Br Alignment identifier is 1/Bs Alignment identifier is 1/Bt Alignment identifier is 1/Bu Alignment identifier is 1/Bv Alignment identifier is 1/Bw Alignment identifier is 1/Bx Alignment identifier is 1/By Alignment identifier is 1/Bz Alignment identifier is 1/B0 Alignment identifier is 1/B1 Alignment identifier is 1/B2 Alignment identifier is 1/B3 Alignment identifier is 1/B4 Alignment identifier is 1/B5 Alignment identifier is 1/B6 Alignment identifier is 1/B7 Alignment identifier is 1/B8 Alignment identifier is 1/B9 Alignment identifier is 1/Baa Alignment identifier is 1/Bab Alignment identifier is 1/Bac Alignment identifier is 1/Bad Alignment identifier is 1/Bae Alignment identifier is 1/Baf Alignment identifier is 1/Bag Alignment identifier is 1/Bah Alignment identifier is 1/Bai Alignment identifier is 1/Baj Alignment identifier is 1/Bak Alignment identifier is 1/Bal Alignment identifier is 1/Bam Alignment identifier is 1/Ban Alignment identifier is 1/Bao Alignment identifier is 1/Bap Alignment identifier is 1/Baq Alignment identifier is 1/Bar Alignment identifier is 1/Bas Alignment identifier is 1/Bat Alignment identifier is 1/Bau Alignment identifier is 1/Bav Alignment identifier is 1/Baw Alignment identifier is 1/Bax Alignment identifier is 1/Bay Alignment identifier is 1/Baz Alignment identifier is 1/Ba0 Alignment identifier is 1/Ba1 Alignment identifier is 1/Ba2 Alignment identifier is 1/Ba3 Alignment identifier is 1/Ba4 Alignment identifier is 1/Ba5 Alignment identifier is 1/Ba6 Alignment identifier is 1/Ba7 Alignment identifier is 1/Ba8 Alignment identifier is 1/Ba9 Alignment identifier is 1/Bba Alignment identifier is 1/Bbb Alignment identifier is 1/Bbc Alignment identifier is 1/Bbd Alignment identifier is 1/Bbe Alignment identifier is 1/Bbf Alignment identifier is 1/Bbg Alignment identifier is 1/Bbh Alignment identifier is 1/Bbi Alignment identifier is 1/Bbj Alignment identifier is 1/Bbk Alignment identifier is 1/Bbl Alignment identifier is 1/Bbm Alignment identifier is 1/Bbn Alignment identifier is 1/Bbo Alignment identifier is 1/Bbp Alignment identifier is 1/Bbq Alignment identifier is 1/Bbr Alignment identifier is 1/Bbs Alignment identifier is 1/Bbt Alignment identifier is 1/Bbu Alignment identifier is 1/Bbv Alignment identifier is 1/Bbw Alignment identifier is 1/Bbx Alignment identifier is 1/Bby Alignment identifier is 1/Bbz Alignment identifier is 1/Bb0 Alignment identifier is 1/Bb1 Alignment identifier is 1/Bb2 Alignment identifier is 1/Bb3 Alignment identifier is 1/Bb4 Alignment identifier is 1/Bb5 Alignment identifier is 1/Bb6 Alignment identifier is 1/Bb7 Alignment identifier is 1/Bb8 Alignment identifier is 1/Bb9 Alignment identifier is 1/Bca Alignment identifier is 1/Bcb Alignment identifier is 1/Bcc Alignment identifier is 1/Bcd Alignment identifier is 1/Bce Alignment identifier is 1/Bcf Alignment identifier is 1/Bcg Alignment identifier is 1/Bch Alignment identifier is 4 Alignment identifier is 1/Bcj Alignment identifier is 1/Bck Alignment identifier is 1/Bcl Alignment identifier is 1/Bcm Alignment identifier is 1/Bcn Alignment identifier is 1/Bco Alignment identifier is 1/Bcp Alignment identifier is 1/Bcq Alignment identifier is 1/Bcr Alignment identifier is 1/Bcs Alignment identifier is 1/Bct Alignment identifier is 1/Bcu Alignment identifier is 1/Bcv Alignment identifier is 1/Bcw Alignment identifier is 1/Bcx Alignment identifier is 1/Bcy Alignment identifier is 1/Bcz Alignment identifier is 1/Bc0 Alignment identifier is 1/Bc1 Alignment identifier is 1/Bc2 Alignment identifier is 1/Bc3 Alignment identifier is 1/Bc4 Alignment identifier is 1/Bc5 Alignment identifier is 1/Bc6 Alignment identifier is 1/Bc7 Alignment identifier is 5 Alignment identifier is 1/Bc9 Alignment identifier is 1/Bda Alignment identifier is 1/Bdb Alignment identifier is 1/Bdc Alignment identifier is 1/Bdd Alignment identifier is 1/Bde Alignment identifier is 1/Bdf Alignment identifier is 1/Bdg Alignment identifier is 1/Bdh Alignment identifier is 1/Bdi Alignment identifier is 1/Bdj Alignment identifier is 1/Bdk Alignment identifier is 1/Bdl Alignment identifier is 1/Bdm Alignment identifier is 1/Bdn Alignment identifier is 1/Bdo Alignment identifier is 1/Bdp Alignment identifier is 1/Bdq Alignment identifier is 1/Bdr Alignment identifier is 1/Bds Alignment identifier is 1/Bdt Alignment identifier is 1/Bdu Alignment identifier is 1/Bdv Alignment identifier is 1/Bdw Alignment identifier is 1/A0 Alignment identifier is 6 Alignment identifier is 1/Bdx Alignment identifier is 1/Bdy Alignment identifier is 1/Bdz Alignment identifier is 1/Aac Alignment identifier is 1/Aah Alignment identifier is 7 Alignment identifier is 8 Alignment identifier is 9 Alignment identifier is 1/Bd0 Alignment identifier is 1/Bd1 Alignment identifier is 1/Bd2 Alignment identifier is 1/Bd3 Alignment identifier is 1/Bd5 Alignment identifier is 1/Bd6 Alignment identifier is 1/Bd7 Alignment identifier is 1/Bd8 Alignment identifier is 1/Bd9 Alignment identifier is 1/Bea Alignment identifier is 1/Beb Alignment identifier is 1/Bec Alignment identifier is 1/Bed Alignment identifier is 1/Bee Alignment identifier is 1/Bef Alignment identifier is 1/Beg Alignment identifier is 1/Beh Alignment identifier is 1/Bei Alignment identifier is 1/Aaw Alignment identifier is 1/Bej Alignment identifier is 1/Bek Alignment identifier is 1/Bel Alignment identifier is 10 Alignment identifier is 1/Aa0 Alignment identifier is 1/Bem Alignment identifier is 1/Ben Alignment identifier is 1/Beo Alignment identifier is 1/Bep Alignment identifier is 1/Beq Alignment identifier is 1/Ber Alignment identifier is 1/Bes Alignment identifier is 1/Bet Alignment identifier is 1/Beu Alignment identifier is 1/Bev Alignment identifier is 1/Bew Alignment identifier is 1/Bex Alignment identifier is 1/Bey Alignment identifier is 11 Alignment identifier is 1/Bez Alignment identifier is 1/Be0 Alignment identifier is 1/Be1 Alignment identifier is 1/Be2 Alignment identifier is 1/Be3 Alignment identifier is 1/Be4 Alignment identifier is 12 Alignment identifier is 1/Abb Alignment identifier is 1/Be5 Alignment identifier is 1/Be6 Alignment identifier is 1/Be7 Alignment identifier is 1/Be8 Alignment identifier is 1/Be9 Alignment identifier is 1/Bfa Alignment identifier is 1/Bfb Alignment identifier is 1/Bfc Alignment identifier is 13 Alignment identifier is 14 Alignment identifier is 1/Bfd Alignment identifier is 1/Bfe Alignment identifier is 1/Bff Alignment identifier is 1/Bfg Alignment identifier is 1/Bfh Alignment identifier is 15 Alignment identifier is 1/Bfj Alignment identifier is 1/Bfk Alignment identifier is 1/Bfl Alignment identifier is 1/Bfm Alignment identifier is 1/Bfn Alignment identifier is 1/Bfo Alignment identifier is 1/Bfp Alignment identifier is 1/Bfr Alignment identifier is 1/Bfs Alignment identifier is 1/Bft Alignment identifier is 16 Alignment identifier is 1/Bfu Alignment identifier is 1/Bfv Alignment identifier is 1/Bfx Alignment identifier is 1/Bfy Alignment identifier is 1/Bfz Alignment identifier is 1/Bf0 Alignment identifier is 1/Bf1 Alignment identifier is 1/Bf2 Alignment identifier is 1/Bf3 Alignment identifier is 17 Alignment identifier is 1/Bf6 Alignment identifier is 1/Bf7 Alignment identifier is 1/Bf8 Alignment identifier is 1/Bga Alignment identifier is 1/Bgb Alignment identifier is 1/Bgc Alignment identifier is 1/Bgd Alignment identifier is 1/Bge Alignment identifier is 1/Bgf Alignment identifier is 1/Bgg Alignment identifier is 18 Alignment identifier is 1/Bgh Alignment identifier is 1/Bgi Alignment identifier is 1/Bgj Alignment identifier is 19 Alignment identifier is 1/Bgl Alignment identifier is 1/Bgm Alignment identifier is 1/Bgn Alignment identifier is 1/Bgo Alignment identifier is 1/Bgp Alignment identifier is 1/Bgq Alignment identifier is 1/Bgr Alignment identifier is 1/Bgs Alignment identifier is 1/Bgt Alignment identifier is 1/Bgu Alignment identifier is 1/Bgv Alignment identifier is 1/Bgw Alignment identifier is 1/Ace Alignment identifier is 1/Bgx Alignment identifier is 1/Bgy Alignment identifier is 20 Alignment identifier is 1/Bg0 Alignment identifier is 1/Bg1 Alignment identifier is 1/Ach Alignment identifier is 1/Ack Alignment identifier is 1/Bg2 Alignment identifier is 1/Bg3 Alignment identifier is 1/Bg4 Alignment identifier is 1/Bg5 Alignment identifier is 1/Bg6 Alignment identifier is 1/Bg8 Alignment identifier is 1/Bg9 Alignment identifier is 1/Bha Alignment identifier is 1/Bhb Alignment identifier is 1/Bhc Alignment identifier is 1/Bhd Alignment identifier is 1/Bhe Alignment identifier is 1/Bhf Alignment identifier is 1/Bhg Alignment identifier is 1/Bhh Alignment identifier is 1/Bhj Alignment identifier is 1/Bhk Alignment identifier is 1/Bhl Alignment identifier is 1/Bhm Alignment identifier is 1/Bhn Alignment identifier is 21 Alignment identifier is 1/Bhp Alignment identifier is 1/Bhq Alignment identifier is 1/Bhr Alignment identifier is 1/Bhs Alignment identifier is 1/Bhu Alignment identifier is 22 Alignment identifier is 1/Bhx Alignment identifier is 1/Bhy Alignment identifier is 23 Alignment identifier is 1/Bhz Alignment identifier is 1/Bh0 Alignment identifier is 1/Bh1 Alignment identifier is 1/Bh2 Alignment identifier is 1/Bh3 Alignment identifier is 1/Ac9 Alignment identifier is 1/Bh4 Alignment identifier is 1/Bh5 Alignment identifier is 1/Bh6 Alignment identifier is 1/Bh7 Alignment identifier is 1/Bh8 Alignment identifier is 1/Bia Alignment identifier is 1/Bib Alignment identifier is 1/Ada Alignment identifier is 24 Alignment identifier is 1/Bic Alignment identifier is 1/Bid Alignment identifier is 1/Bif Alignment identifier is 1/Ade Alignment identifier is 1/Adj Alignment identifier is 1/Big Alignment identifier is 1/Bih Alignment identifier is 1/Bii Alignment identifier is 25 Alignment identifier is 1/Bij Alignment identifier is 26 Alignment identifier is 1/Bil Alignment identifier is 1/Bim Alignment identifier is 1/Bio Alignment identifier is 1/Bip Alignment identifier is 1/Biq Alignment identifier is 27 Alignment identifier is 1/Bir Alignment identifier is 1/Bis Alignment identifier is 1/Bit Alignment identifier is 1/Biu Alignment identifier is 1/Biw Alignment identifier is 1/Bix Alignment identifier is 1/Adz Alignment identifier is 1/Biy Alignment identifier is 1/Bi0 Alignment identifier is 1/Bi1 Alignment identifier is 1/Bi2 Alignment identifier is 1/Bi3 Alignment identifier is 1/Bi4 Alignment identifier is 1/Bi5 Alignment identifier is 1/Bi6 Alignment identifier is 1/Bi7 Alignment identifier is 1/Bi8 Alignment identifier is 28 Alignment identifier is 1/Bjc Alignment identifier is 1/Bjd Alignment identifier is 1/Ad6 Alignment identifier is 1/Bjg Alignment identifier is 1/Bjh Alignment identifier is 1/Bjk Alignment identifier is 1/Bjl Alignment identifier is 1/Bjm Alignment identifier is 1/Ad7 ===== Log before crash end ===== Log: > set bgColor white > cofr centerOfView UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class001.mrc"" Opened run_it025_class001.mrc as #1, grid size 200,200,200, pixel 3.12, shown at level 7.89e-06, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class002.mrc"" Opened run_it025_class002.mrc as #2, grid size 200,200,200, pixel 3.12, shown at level 1.62e-05, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class003.mrc"" Opened run_it025_class003.mrc as #3, grid size 200,200,200, pixel 3.12, shown at level 8.28e-06, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class004.mrc"" Opened run_it025_class004.mrc as #4, grid size 200,200,200, pixel 3.12, shown at level 1.4e-06, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class005.mrc"" Opened run_it025_class005.mrc as #5, grid size 200,200,200, pixel 3.12, shown at level 2.84e-06, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class006.mrc"" Opened run_it025_class006.mrc as #6, grid size 200,200,200, pixel 3.12, shown at level 1.84e-05, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class007.mrc"" Opened run_it025_class007.mrc as #7, grid size 200,200,200, pixel 3.12, shown at level 2.04e-05, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class008.mrc"" Opened run_it025_class008.mrc as #8, grid size 200,200,200, pixel 3.12, shown at level 5.79e-06, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class009.mrc"" Opened run_it025_class009.mrc as #9, grid size 200,200,200, pixel 3.12, shown at level 8.44e-06, step 1, values float32 > open ""/Users/c.lewis.2/Desktop/VP2 > paper/Focused_class/VS4_peptide/CC/run_it025_class010.mrc"" Opened run_it025_class010.mrc as #10, grid size 200,200,200, pixel 3.12, shown at level 1.91e-05, step 1, values float32 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 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AU001HUB/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 5 hours, 4 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: HP Z24n G3: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 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 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 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: 2.5.1 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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: 1.45.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 MolecularDynamicsViewer: 1.6 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX