id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7294 Pseudobond reader not bulletproof to loop pseudobonds andrew.plested@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Trying to save after opening pb file Fatal Python error: Segmentation fault Thread 0x00000003259c1000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003249be000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003239bb000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003229b8000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003219b5000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003209b2000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031f9af000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031e9ac000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031d9a9000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031c9a6000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031b9a3000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031a9a0000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031999d000 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x000000020517c600 (most recent call first): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py"", line 499 in _delete_group File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/pbgroup.py"", line 41 in delete File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1189 in __del__ File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 870 in init File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1021 in File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2022-07-18 17:22:16.00 +0200"",""app_version"":""1.4.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.4.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.2.1 (21D62)"",""incident_id"":""CAA985F2-84D5-4597-B0AF-AFE76F5AD3D5"",""name"":""ChimeraX""} { ""uptime"" : 840000, ""procLaunch"" : ""2022-07-11 21:53:38.3012 +0200"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,4"", ""procStartAbsTime"" : 14083132641527, ""coalitionID"" : 38419, ""osVersion"" : { ""train"" : ""macOS 12.2.1"", ""build"" : ""21D62"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-07-18 17:22:04.6120 +0200"", ""incident"" : ""CAA985F2-84D5-4597-B0AF-AFE76F5AD3D5"", ""bug_type"" : ""309"", ""pid"" : 1810, ""procExitAbsTime"" : 20254980544369, ""translated"" : true, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.4.0"",""CFBundleVersion"":""1.4.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""84BBF05B-B828-5F12-85DC-AC877EEADB38"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""39FD42C9-AED2-B74F-E345-248A982B14F1"", ""wakeTime"" : 5602, ""sleepWakeUUID"" : ""7C15864A-CA61-43D5-9E8C-C863F7AE6C8C"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x3ce3058b6018 is not in any region. Bytes after previous region: 66464711925785 Bytes before following region: 38607368003560\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV "", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x00003ce3058b6018"",""rawCodes"":[1,66945748262936],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00003ce3058b6018""}, ""vmregioninfo"" : ""0x3ce3058b6018 is not in any region. 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""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""61fb0e87c773c43cde3bb80e"" }, ""deploymentId"" : 240000303 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""622657ce37186c771d5404ad"" }, ""deploymentId"" : 240000416 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000167 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : { ""SIRI_VALUE_INFERENCE_CONTACT_RESOLUTION"" : ""62bdc4218fe09c1632d841e9"" }, ""deploymentId"" : 240000023 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000401 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/first run with one > set/active_R close > open ""/Users/Andrew/Nextcloud/CaMKII/modelling > crosslinks/active_R>1/IHP_R>1.cxs"" format session No such file/path: /Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/active_R>1/IHP_R>1.cxs > open ""/Users/Andrew/Nextcloud/CaMKII/modelling > crosslinks/active_R>1/IHP_R>1.cxs"" format session No such file/path: /Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/active_R>1/IHP_R>1.cxs > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/first run with one > set/active_R>1/IHP_R>1.cxs"" opened ChimeraX session > show #5 models > hide #5 models > hide #6 models > select #4/A:37 17 atoms, 16 bonds, 1 residue, 1 model selected > select #A/3:137 Expected an objects specifier or a keyword > select #3/B:37 17 atoms, 16 bonds, 1 residue, 1 model selected > surface hidePatches (#!3 & sel) > open /Users/Andrew/Desktop/active30.pb Line 0 ""#4/A:137 #3/B:47 "", got 22 atoms for spec ""#4/A:137"", require exactly 1 > open /Users/Andrew/Desktop/active30.pb Opened Pseudobonds active30.pb, 20 bonds > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/Active_30min.cxs"" > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,34.868,0,1,0,-6.9818,0,0,1,-67.117 > undo > select add #4 7265 atoms, 7348 bonds, 11 pseudobonds, 460 residues, 5 models selected > select add #3 14499 atoms, 14667 bonds, 22 pseudobonds, 918 residues, 7 models selected > select subtract #3 7248 atoms, 7332 bonds, 11 pseudobonds, 459 residues, 5 models selected > select add #1 94445 atoms, 95537 bonds, 23 pseudobonds, 5967 residues, 12 models selected > view matrix models > #1,0.75305,-0.65519,0.060313,138.35,0.65568,0.73965,-0.15162,126.1,0.054732,0.15373,0.9866,-105.7,#4,1,0,0,6.1521,0,1,0,-16.259,0,0,1,-17.612,#5,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.75305,-0.65519,0.060313,152.86,0.65568,0.73965,-0.15162,133.99,0.054732,0.15373,0.9866,-111.24,#4,1,0,0,20.668,0,1,0,-8.372,0,0,1,-23.152,#5,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.75305,-0.65519,0.060313,156.95,0.65568,0.73965,-0.15162,130.89,0.054732,0.15373,0.9866,-112.35,#4,1,0,0,24.757,0,1,0,-11.465,0,0,1,-24.269,#5,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.75305,-0.65519,0.060313,169.43,0.65568,0.73965,-0.15162,121.52,0.054732,0.15373,0.9866,-112.32,#4,1,0,0,37.236,0,1,0,-20.834,0,0,1,-24.233,#5,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.75305,-0.65519,0.060313,167.22,0.65568,0.73965,-0.15162,119.04,0.054732,0.15373,0.9866,-116,#4,1,0,0,35.031,0,1,0,-23.32,0,0,1,-27.914,#5,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.75305,-0.65519,0.060313,159.71,0.65568,0.73965,-0.15162,101.54,0.054732,0.15373,0.9866,-115,#4,1,0,0,27.512,0,1,0,-40.823,0,0,1,-26.91,#5,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.75305,-0.65519,0.060313,155.71,0.65568,0.73965,-0.15162,93.825,0.054732,0.15373,0.9866,-116.87,#4,1,0,0,23.512,0,1,0,-48.532,0,0,1,-28.781,#5,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.62871,-0.77659,0.040349,230.02,0.76857,0.61264,-0.18433,107.08,0.11843,0.1469,0.98204,-131.48,#4,0.9847,-0.16829,-0.045164,119.83,0.16626,0.98503,-0.045617,-59.143,0.052165,0.03741,0.99794,-55.802,#5,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #1,0.63102,-0.76398,0.13472,199.44,0.76537,0.58478,-0.26878,139.4,0.12656,0.27272,0.95373,-161.07,#4,0.98387,-0.17176,0.050012,98.231,0.17701,0.97513,-0.13339,-34.568,-0.025858,0.14009,0.9898,-90.405,#5,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.63102,-0.76398,0.13472,183.41,0.76537,0.58478,-0.26878,152.3,0.12656,0.27272,0.95373,-145.01,#4,0.98387,-0.17176,0.050012,82.208,0.17701,0.97513,-0.13339,-21.669,-0.025858,0.14009,0.9898,-74.35,#5,1,0,0,0,0,1,0,0,0,0,1,0 > ui mousemode right zoom > ui mousemode right select > select clear > ui mousemode right zoom > save /Users/Andrew/Desktop/image7.png supersample 3 > ui tool show ""Side View"" > save /Users/Andrew/Desktop/image8.png supersample 3 > ui mousemode right zoom > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/active150.pb"" Opened Pseudobonds active150.pb, 43 bonds > hide #7 models > show #7 models > hide #7 models > undo > show #7 models > hide #8 models > select add #2 87197 atoms, 88205 bonds, 12 pseudobonds, 5508 residues, 24 models selected > select add #1 174394 atoms, 176410 bonds, 24 pseudobonds, 11016 residues, 60 models selected > transparency 50 > transparency 30 > transparency 70 > transparency cartoon 70 Missing or invalid ""percent"" argument: Expected a number > show #8 models > hide #7 models > hide #8 models > show #7 models > show #8 models > hide #8 models > show #8 models > hide #7 models > transparency 70 cartoons > transparency 0 cartoons > transparency sel 70 cartoons > transparency sel 50 cartoons > transparency sel 70 > transparency sel 80 > transparency sel 20 cartoons > transparency #1 20 cartoons > transparency #1 20 > transparency #1 0 cartoons > transparency #1 90 cartoons > transparency #1 10 cartoons > transparency #1 70 surfaces > transparency #1 70 cs Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #1 70 cartoons & s Expected ',' or a keyword > transparency #1 70 cartoons, surfaces > transparency sel 70 cartoons, surfaces > surface hidePatches (#!1-2 & sel) > transparency sel 70 cartoons, surfaces > transparency sel 20 cartoons, surfaces > transparency sel 50 cartoons, surfaces > surface (#!1-2 & sel) > surface (#3-4) > surface (#3-4) hide Expected a keyword > hide surfaces (#3-4) Expected ',' or a keyword > hide (#3-4) surfaces > close > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/Active_30min.cxs"" format session opened ChimeraX session > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/active150.pb"" Opened Pseudobonds active150.pb, 43 bonds > hide #7 models > select add #1 87214 atoms, 88221 bonds, 12 pseudobonds, 5509 residues, 9 models selected > select add #4 94462 atoms, 95553 bonds, 23 pseudobonds, 5968 residues, 24 models selected > select add #3 101696 atoms, 102872 bonds, 34 pseudobonds, 6426 residues, 26 models selected > select subtract #3 94445 atoms, 95537 bonds, 23 pseudobonds, 5967 residues, 25 models selected > select add #5 94445 atoms, 95537 bonds, 54 pseudobonds, 5967 residues, 24 models selected > select subtract #5 94445 atoms, 95537 bonds, 13 pseudobonds, 5967 residues, 23 models selected > close #5 > close #6 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.75305,-0.65519,0.060313,142.97,0.65568,0.73965,-0.15162,125.39,0.054732,0.15373,0.9866,-102.5,#4,1,0,0,10.772,0,1,0,-16.972,0,0,1,-14.415 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.4951,-0.85845,0.13396,251.38,0.86844,0.49363,-0.046309,105.31,-0.026373,0.13926,0.9899,-76.699,#4,0.94336,-0.33064,0.027295,176.15,0.32776,0.94156,0.077728,-65.212,-0.0514,-0.064379,0.9966,27.047 > view matrix models > #1,0.37665,-0.91372,0.1525,294.78,0.9245,0.38119,0.00055661,107.99,-0.058639,0.14077,0.9883,-67.653,#4,0.8915,-0.45199,0.030606,243.97,0.44647,0.88804,0.10975,-67.783,-0.076784,-0.084175,0.99349,41.992 > view matrix models > #1,0.49754,-0.82462,0.26918,203.32,0.86673,0.48514,-0.11582,127.62,-0.035087,0.29093,0.9561,-107.27,#4,0.93119,-0.32452,0.16604,141.05,0.32784,0.9447,0.0077523,-49.524,-0.15938,0.047217,0.98609,-6.0646 > view matrix models > #1,0.32769,-0.88039,0.34283,245.79,0.94406,0.31937,-0.082211,143.03,-0.037112,0.35059,0.93579,-117.73,#4,0.84427,-0.48831,0.22083,223.15,0.49671,0.86769,0.019657,-44.428,-0.20121,0.093092,0.97511,-18.488 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.32769,-0.88039,0.34283,234.01,0.94406,0.31937,-0.082211,133.99,-0.037112,0.35059,0.93579,-113.32,#4,0.84427,-0.48831,0.22083,211.37,0.49671,0.86769,0.019657,-53.468,-0.20121,0.093092,0.97511,-14.084 > view matrix models > #1,0.32769,-0.88039,0.34283,215.65,0.94406,0.31937,-0.082211,140.51,-0.037112,0.35059,0.93579,-112.96,#4,0.84427,-0.48831,0.22083,193.01,0.49671,0.86769,0.019657,-46.942,-0.20121,0.093092,0.97511,-13.725 > view matrix models > #1,0.32769,-0.88039,0.34283,214.33,0.94406,0.31937,-0.082211,134.7,-0.037112,0.35059,0.93579,-110.96,#4,0.84427,-0.48831,0.22083,191.69,0.49671,0.86769,0.019657,-52.757,-0.20121,0.093092,0.97511,-11.716 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.20851,-0.88247,0.42164,226.13,0.9779,0.18145,-0.10385,169.96,0.015136,0.43397,0.9008,-139.12,#4,0.76064,-0.57993,0.29174,233.84,0.61126,0.79115,-0.021038,-25.326,-0.21861,0.19433,0.95627,-53.652 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.20851,-0.88247,0.42164,216,0.9779,0.18145,-0.10385,170.68,0.015136,0.43397,0.9008,-136.91,#4,0.76064,-0.57993,0.29174,223.7,0.61126,0.79115,-0.021038,-24.6,-0.21861,0.19433,0.95627,-51.446 > view matrix models > #1,0.20851,-0.88247,0.42164,204.83,0.9779,0.18145,-0.10385,163.23,0.015136,0.43397,0.9008,-131.1,#4,0.76064,-0.57993,0.29174,212.54,0.61126,0.79115,-0.021038,-32.054,-0.21861,0.19433,0.95627,-45.633 > view matrix models > #1,0.20851,-0.88247,0.42164,209.36,0.9779,0.18145,-0.10385,162.22,0.015136,0.43397,0.9008,-146.54,#4,0.76064,-0.57993,0.29174,217.07,0.61126,0.79115,-0.021038,-33.061,-0.21861,0.19433,0.95627,-61.077 > view matrix models > #1,0.20851,-0.88247,0.42164,206.71,0.9779,0.18145,-0.10385,163.08,0.015136,0.43397,0.9008,-138.23,#4,0.76064,-0.57993,0.29174,214.42,0.61126,0.79115,-0.021038,-32.207,-0.21861,0.19433,0.95627,-52.767 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.25914,-0.91641,0.30502,234.76,0.95697,0.28633,0.047235,97.193,-0.13062,0.27965,0.95118,-68.357,#4,0.81397,-0.55417,0.17423,221.4,0.53589,0.83209,0.14299,-79.507,-0.22422,-0.023022,0.97427,50.38 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.25914,-0.91641,0.30502,234.33,0.95697,0.28633,0.047235,99.499,-0.13062,0.27965,0.95118,-73.003,#4,0.81397,-0.55417,0.17423,220.96,0.53589,0.83209,0.14299,-77.201,-0.22422,-0.023022,0.97427,45.733 > ui mousemode right zoom > ui mousemode right translate > ui mousemode right select > select clear > show #7 models > hide #8 models > save /Users/Andrew/Desktop/image7.png supersample 3 > show #8 models > hide #7 models > save /Users/Andrew/Desktop/image8.png supersample 3 > ui mousemode right zoom > select add #4 7248 atoms, 7332 bonds, 1 pseudobond, 459 residues, 2 models selected > select add #1 94445 atoms, 95537 bonds, 13 pseudobonds, 5967 residues, 11 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.25914,-0.91641,0.30502,234.88,0.95697,0.28633,0.047235,101.09,-0.13062,0.27965,0.95118,-76.277,#4,0.81397,-0.55417,0.17423,221.52,0.53589,0.83209,0.14299,-75.612,-0.22422,-0.023022,0.97427,42.46 > view matrix models > #1,0.25914,-0.91641,0.30502,234.81,0.95697,0.28633,0.047235,103.72,-0.13062,0.27965,0.95118,-80.56,#4,0.81397,-0.55417,0.17423,221.45,0.53589,0.83209,0.14299,-72.978,-0.22422,-0.023022,0.97427,38.177 > ui mousemode right ""rotate selected models"" > ui mousemode right rotate > ui mousemode right ""translate selected models"" > view matrix models > #1,0.25914,-0.91641,0.30502,226.53,0.95697,0.28633,0.047235,105.12,-0.13062,0.27965,0.95118,-82.289,#4,0.81397,-0.55417,0.17423,213.17,0.53589,0.83209,0.14299,-71.582,-0.22422,-0.023022,0.97427,36.448 > view matrix models > #1,0.25914,-0.91641,0.30502,226.47,0.95697,0.28633,0.047235,105.12,-0.13062,0.27965,0.95118,-82.276,#4,0.81397,-0.55417,0.17423,213.11,0.53589,0.83209,0.14299,-71.578,-0.22422,-0.023022,0.97427,36.46 > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/Active_30_150.cxs"" > ui mousemode right zoom > ui mousemode right select > select clear > ui mousemode right rotate > ui mousemode right translate > show #7 models > hide #8 models > save /Users/Andrew/Desktop/image9.png supersample 3 > show #8 models > hide #7 models > save /Users/Andrew/Desktop/image10.png supersample 3 > ui mousemode right zoom > hide #8 models > show #7 models > save /Users/Andrew/Desktop/image7.png supersample 3 > show #8 models > hide #7 models > save /Users/Andrew/Desktop/image8.png supersample 3 > select clear > save /Users/Andrew/Desktop/image7.png supersample 3 > show #7 models > hide #8 models > save /Users/Andrew/Desktop/image8.png supersample 3 > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/Active_30_150.cxs"" > close > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/first run with one > set/active_R open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/basal_30.pb"" Opened Pseudobonds basal_30.pb, 3 bonds > hide #11 models > hide #10 models > hide #9 models > close #3, #5 Expected a models specifier or a keyword > close #3 > close #5 > close #6 > close #8 > close #9 > close #10 > close #11 > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/Basal_30_150.cxs"" > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/basal_150.pb"" Opened Pseudobonds basal_150.pb, 8 bonds > hide #12 models > show #12 models > hide #3 models > save /Users/Andrew/Desktop/image7.png supersample 3 > show #3 models > hide #12 models > save /Users/Andrew/Desktop/image8.png supersample 3 > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_basal_30_150_within_holo.cxs"" > close > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/Active_30_150.cxs"" format session No such file/path: /Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd analyses/Active_30_150.cxs > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/Active_30_150.cxs"" format session No such file/path: /Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd analyses/Active_30_150.cxs > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_Active_30_150.cxs"" opened ChimeraX session > close #7 > close #8 > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_basal_30_IHP.pb"" ""/Users/Andrew/Nextcloud/CaMKII/modelling > crosslinks/2nd analyses/het_basal_150_IHP.pb"" Opened Pseudobonds het_basal_30_IHP.pb, 3 bonds Opened Pseudobonds het_basal_150_IHP.pb, 8 bonds > hide #6 models > show #6 models > hide #5 models > show #5 models > hide #5 models > undo > select add #4 7248 atoms, 7332 bonds, 1 pseudobond, 459 residues, 2 models selected > select add #1 94445 atoms, 95537 bonds, 13 pseudobonds, 5967 residues, 11 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.25914,-0.91641,0.30502,228.45,0.95697,0.28633,0.047235,63.082,-0.13062,0.27965,0.95118,-10.962,#4,0.81397,-0.55417,0.17423,215.09,0.53589,0.83209,0.14299,-113.62,-0.22422,-0.023022,0.97427,107.77 > view matrix models > #1,0.25914,-0.91641,0.30502,236.92,0.95697,0.28633,0.047235,90.881,-0.13062,0.27965,0.95118,11.455,#4,0.81397,-0.55417,0.17423,223.56,0.53589,0.83209,0.14299,-85.819,-0.22422,-0.023022,0.97427,130.19 > view matrix models > #1,0.25914,-0.91641,0.30502,238.95,0.95697,0.28633,0.047235,90.727,-0.13062,0.27965,0.95118,32.425,#4,0.81397,-0.55417,0.17423,225.59,0.53589,0.83209,0.14299,-85.973,-0.22422,-0.023022,0.97427,151.16 > view matrix models > #1,0.25914,-0.91641,0.30502,239.19,0.95697,0.28633,0.047235,92.138,-0.13062,0.27965,0.95118,43.845,#4,0.81397,-0.55417,0.17423,225.82,0.53589,0.83209,0.14299,-84.562,-0.22422,-0.023022,0.97427,162.58 > view matrix models > #1,0.25914,-0.91641,0.30502,222.37,0.95697,0.28633,0.047235,82.944,-0.13062,0.27965,0.95118,59.268,#4,0.81397,-0.55417,0.17423,209.01,0.53589,0.83209,0.14299,-93.756,-0.22422,-0.023022,0.97427,178 > view matrix models > #1,0.25914,-0.91641,0.30502,215.01,0.95697,0.28633,0.047235,117.8,-0.13062,0.27965,0.95118,58.333,#4,0.81397,-0.55417,0.17423,201.65,0.53589,0.83209,0.14299,-58.898,-0.22422,-0.023022,0.97427,177.07 > ui mousemode right zoom > crosslinks minimize #6 moveModels (#1 & #4) No structures specified for minimizing crosslinks. > crosslinks minimize #6 moveModels (#1,4) 8 crosslinks, lengths: 42.8, 42.3, 34.5, 32.7, 32.3, 26.9, 24.8, 16.6 > undo > ui mousemode right ""translate selected models"" > view matrix models > #1,0.25914,-0.91641,0.30502,183.46,0.95697,0.28633,0.047235,25.673,-0.13062,0.27965,0.95118,-92.2,#4,0.81397,-0.55417,0.17423,170.1,0.53589,0.83209,0.14299,-151.03,-0.22422,-0.023022,0.97427,26.537 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.38508,-0.63455,-0.67011,342.18,0.65902,0.69739,-0.28167,85.927,0.64606,-0.33315,0.68674,-63.788,#4,0.66533,-0.11525,-0.7376,205.67,0.022364,0.99065,-0.13462,-69.913,0.74622,0.073069,0.66168,-114.55 > view matrix models > #1,-0.52966,0.32799,-0.78223,359.8,0.22986,0.94321,0.23984,-8.7858,0.81647,-0.052771,-0.57497,162.99,#4,-0.66093,0.013915,-0.75032,379.09,-0.43042,0.812,0.3942,-32.757,0.61474,0.58349,-0.53069,-48.088 > view matrix models > #1,-0.52911,0.32745,-0.78282,359.96,0.22796,0.94348,0.24058,-8.536,0.81736,-0.051157,-0.57385,161.98,#4,-0.66021,0.013963,-0.75095,379.1,-0.43199,0.81084,0.39487,-32.077,0.61442,0.5851,-0.52929,-49.163 > view matrix models > #1,-0.76437,0.29146,-0.57514,377.53,0.21601,0.95621,0.19749,3.3042,0.60752,0.026722,-0.79386,260.36,#4,-0.80126,-0.19841,-0.56446,461.98,-0.45193,0.81895,0.35366,-22.385,0.3921,0.53847,-0.74586,66.177 > view matrix models > #1,-0.87274,0.30344,-0.38242,350.84,0.18585,0.93089,0.31449,-13.777,0.45142,0.20339,-0.86882,275.55,#4,-0.87909,-0.28982,-0.37842,474.97,-0.45099,0.76271,0.46355,-21.905,0.15428,0.57816,-0.8012,102.27 > view matrix models > #1,-0.94505,0.26696,-0.1887,327.07,0.148,0.86404,0.48118,-31.11,0.2915,0.42681,-0.85607,254.13,#4,-0.89796,-0.39358,-0.19686,484.46,-0.42564,0.66317,0.61566,-15.02,-0.11176,0.63663,-0.76303,111.07 > view matrix models > #1,-0.98979,0.093857,0.10723,305.24,0.13267,0.88158,0.45301,-23.855,-0.052015,0.46261,-0.88503,348.26,#4,-0.80039,-0.59583,0.066049,501.68,-0.45037,0.67037,0.58972,-7.8041,-0.39565,0.44226,-0.8049,266.7 > view matrix models > #1,-0.93774,0.29404,0.18491,212.9,0.29769,0.95463,-0.008331,38.64,-0.17897,0.047233,-0.98272,527.38,#4,-0.88766,-0.42541,0.17631,406.34,-0.40179,0.90255,0.15483,-23.092,-0.22499,0.066593,-0.97208,462.02 > crosslinks minimize #6 moveModels (#1-4) 8 crosslinks, lengths: 42.8, 42.3, 34.5, 32.7, 32.3, 26.9, 24.8, 16.6 > undo > crosslinks minimize #6 moveModels (sel) 8 crosslinks, lengths: 42.8, 42.3, 34.5, 32.7, 32.3, 26.9, 24.8, 16.6 > close > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_Active_30_150.cxs"" format session opened ChimeraX session > close #7 > close #8 > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_basal_30_IHP.pb"" ""/Users/Andrew/Nextcloud/CaMKII/modelling > crosslinks/2nd analyses/het_basal_150_IHP.pb"" Opened Pseudobonds het_basal_30_IHP.pb, 3 bonds Opened Pseudobonds het_basal_150_IHP.pb, 8 bonds > select add #4 7248 atoms, 7332 bonds, 1 pseudobond, 459 residues, 2 models selected > select subtract #4 1 model selected > select add #4 7248 atoms, 7332 bonds, 1 pseudobond, 459 residues, 2 models selected > select add #1 94445 atoms, 95537 bonds, 13 pseudobonds, 5967 residues, 11 models selected > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_basal_30_150_IHP.cxs"" > hide #5 models > hide #6 models > show #5 models > hide #5 models > show #6 models > crosslinks minimize #6 moveModels (#1,#4) Invalid ""moveModels"" argument: invalid structures specifier > crosslinks minimize #6 moveModels (#1,4) 8 crosslinks, lengths: 42.8, 42.3, 34.5, 32.7, 32.3, 26.9, 24.8, 16.6 > align #4/A movemodels #1 Expected a keyword > align #1 toAtoms #4/A move #1 Invalid ""move"" argument: Should be one of 'atoms', 'chains', 'nothing', 'residues', 'structure atoms', or 'structures' > align #1 toAtoms #4/A move structures #1 Expected a keyword > align #1/A toAtoms #4/A move structures RMSD between 7248 atom pairs is 0.000 angstroms > view matrix models > #1,-0.35755,-0.74604,0.56177,290.85,0.27276,0.49189,0.82683,-43.368,-0.89317,0.44886,0.027615,352.36,#4,0.25343,-0.87143,0.41999,418.4,-0.067012,0.41731,0.90629,-14.085,-0.96503,-0.25783,0.047361,520.81 > undo > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.1951,-0.7291,0.65601,211.74,0.48167,0.51142,0.71165,-73.419,-0.85436,0.45482,0.25141,280.95,#4,0.37035,-0.76667,0.52445,318.12,0.070566,0.58619,0.80709,-95.103,-0.92621,-0.2619,0.2712,464.56 > view matrix models > #1,-0.1951,-0.7291,0.65601,211.6,0.48167,0.51142,0.71165,-71.763,-0.85436,0.45482,0.25141,284.41,#4,0.37035,-0.76667,0.52445,317.98,0.070566,0.58619,0.80709,-93.447,-0.92621,-0.2619,0.2712,468.02 > view matrix models > #1,-0.1951,-0.7291,0.65601,211.47,0.48167,0.51142,0.71165,-69.893,-0.85436,0.45482,0.25141,289.04,#4,0.37035,-0.76667,0.52445,317.85,0.070566,0.58619,0.80709,-91.577,-0.92621,-0.2619,0.2712,472.65 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.22307,-0.6949,0.68363,201.98,0.43113,0.55866,0.70854,-68.119,-0.87428,0.45278,0.17497,316.57,#4,0.32855,-0.7639,0.55544,316.22,0.0013625,0.58846,0.80852,-80.852,-0.94449,-0.26488,0.19438,496.25 > view matrix models > #1,-0.22436,-0.69768,0.68037,204.04,0.42634,0.55754,0.71231,-67.521,-0.8763,0.44988,0.17236,318.67,#4,0.3292,-0.76631,0.55172,318.21,-0.0012811,0.58392,0.81181,-78.968,-0.94426,-0.26795,0.19124,498.49 > view matrix models > #1,-0.21868,-0.68577,0.69419,195.25,0.44667,0.56215,0.69604,-69.945,-0.86756,0.46228,0.18338,309.67,#4,0.32651,-0.75587,0.5675,309.68,0.010023,0.60314,0.79758,-86.877,-0.94514,-0.25472,0.2045,488.89 > zoom Pixel size at center of rotation is 0.252 > ui mousemode right zoom > ui mousemode right select > select clear > ui mousemode right zoom > show #5 models > hide #6 models > hide #5 models > save /Users/Andrew/Desktop/image7.png supersample 3 > show #6 models > ui tool show ""Side View"" > save /Users/Andrew/Desktop/image7.png supersample 3 > show #5 models > hide #6 models > hide #5 models > show #5 models > save /Users/Andrew/Desktop/image7.png supersample 3 > view > save /Users/Andrew/Desktop/image8.png supersample 3 > show #6 models > hide #5 models > save /Users/Andrew/Desktop/image9.png supersample 3 > show #5 models > hide #6 models > save /Users/Andrew/Desktop/image10.png supersample 3 > show #6 models > hide #5 models > save /Users/Andrew/Desktop/image11.png supersample 3 > select add #3 7251 atoms, 7335 bonds, 1 pseudobond, 459 residues, 2 models selected > select add #2 94448 atoms, 95540 bonds, 13 pseudobonds, 5967 residues, 5 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,1,0,0,0.05347,0,1,0,-0.026049,0,0,1,-0.093687,#3,1,0,0,0.05347,0,1,0,-0.026049,0,0,1,-0.093687 > view matrix models > #2,1,0,0,1.4531,0,1,0,-0.92785,0,0,1,-4.4644,#3,1,0,0,1.4531,0,1,0,-0.92785,0,0,1,-4.4644 > view matrix models > #2,1,0,0,2.1494,0,1,0,-1.5287,0,0,1,-7.9664,#3,1,0,0,2.1494,0,1,0,-1.5287,0,0,1,-7.9664 > view matrix models > #2,1,0,0,1.4544,0,1,0,-0.88128,0,0,1,-4.0548,#3,1,0,0,1.4544,0,1,0,-0.88128,0,0,1,-4.0548 > view matrix models > #2,1,0,0,1.7296,0,1,0,-1.8112,0,0,1,-11.479,#3,1,0,0,1.7296,0,1,0,-1.8112,0,0,1,-11.479 > view matrix models > #2,1,0,0,3.885,0,1,0,-2.6464,0,0,1,-16.509,#3,1,0,0,3.885,0,1,0,-2.6464,0,0,1,-16.509 > view matrix models > #2,1,0,0,8.8149,0,1,0,0.52448,0,0,1,-10.586,#3,1,0,0,8.8149,0,1,0,0.52448,0,0,1,-10.586 > view matrix models > #2,1,0,0,6.8968,0,1,0,4.0112,0,0,1,-2.6212,#3,1,0,0,6.8968,0,1,0,4.0112,0,0,1,-2.6212 > view matrix models > #2,1,0,0,9.0141,0,1,0,7.4782,0,0,1,-4.8523,#3,1,0,0,9.0141,0,1,0,7.4782,0,0,1,-4.8523 > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.98085,0.035879,-0.19145,57.898,-0.033061,0.99929,0.017893,11.928,0.19196,-0.011221,0.98134,-50.271,#3,0.98085,0.035879,-0.19145,57.898,-0.033061,0.99929,0.017893,11.928,0.19196,-0.011221,0.98134,-50.271 > view matrix models > #2,0.97832,0.038098,-0.20356,61.365,-0.034589,0.99919,0.020768,11.584,0.20418,-0.013277,0.97884,-52.428,#3,0.97832,0.038098,-0.20356,61.365,-0.034589,0.99919,0.020768,11.584,0.20418,-0.013277,0.97884,-52.428 > view matrix models > #2,0.97325,0.063094,-0.22092,60.577,-0.08436,0.99253,-0.088175,57.825,0.21371,0.10445,0.9713,-86.084,#3,0.97325,0.063094,-0.22092,60.577,-0.08436,0.99253,-0.088175,57.825,0.21371,0.10445,0.9713,-86.084 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.97325,0.063094,-0.22092,63.761,-0.08436,0.99253,-0.088175,52.757,0.21371,0.10445,0.9713,-79.904,#3,0.97325,0.063094,-0.22092,63.761,-0.08436,0.99253,-0.088175,52.757,0.21371,0.10445,0.9713,-79.904 > ~clashes > clashes #3 33807 clashes > hide #!1 models > clashes #3 33807 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,37.616,-0.08436,0.99253,-0.088175,39.015,0.21371,0.10445,0.9713,-89.43,#3,0.97325,0.063094,-0.22092,37.616,-0.08436,0.99253,-0.088175,39.015,0.21371,0.10445,0.9713,-89.43 > clashes #3 35937 clashes > clashes #4 34165 clashes > show #!1 models > clashes #3 35937 clashes > clashes #3 name Cl3 35937 clashes > hide #7 models > hide #6 models > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > show bonds #8 Expected ',' or a keyword > show #8 bonds > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > show #!3 models > show #!4 models > clashes #3 restrict #1 name Cl3 2006 clashes > ui mousemode right ""translate selected models"" > view matrix models > #2,0.97325,0.063094,-0.22092,39.751,-0.08436,0.99253,-0.088175,42,0.21371,0.10445,0.9713,-87.743,#3,0.97325,0.063094,-0.22092,39.751,-0.08436,0.99253,-0.088175,42,0.21371,0.10445,0.9713,-87.743 > clashes #3 restrict #1 name Cl3 1755 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,44.71,-0.08436,0.99253,-0.088175,40.491,0.21371,0.10445,0.9713,-85.974,#3,0.97325,0.063094,-0.22092,44.71,-0.08436,0.99253,-0.088175,40.491,0.21371,0.10445,0.9713,-85.974 > clashes #3 restrict #1 name Cl3 1879 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,38.75,-0.08436,0.99253,-0.088175,45.347,0.21371,0.10445,0.9713,-87.302,#3,0.97325,0.063094,-0.22092,38.75,-0.08436,0.99253,-0.088175,45.347,0.21371,0.10445,0.9713,-87.302 > clashes #3 restrict #1 name Cl3 1284 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,37.507,-0.08436,0.99253,-0.088175,46.01,0.21371,0.10445,0.9713,-81.76,#3,0.97325,0.063094,-0.22092,37.507,-0.08436,0.99253,-0.088175,46.01,0.21371,0.10445,0.9713,-81.76 > select up 94448 atoms, 95540 bonds, 13 pseudobonds, 5967 residues, 17 models selected > select down 94448 atoms, 95540 bonds, 1 pseudobond, 5967 residues, 16 models selected > select up 94448 atoms, 95540 bonds, 13 pseudobonds, 5967 residues, 17 models selected > select down 94448 atoms, 95540 bonds, 1 pseudobond, 5967 residues, 16 models selected > select down 94448 atoms, 95540 bonds, 1 pseudobond, 5967 residues, 16 models selected > select up 94448 atoms, 95540 bonds, 13 pseudobonds, 5967 residues, 17 models selected > select down 94448 atoms, 95540 bonds, 1 pseudobond, 5967 residues, 16 models selected > clashes #3 restrict #1 name Cl3 747 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.544,-0.08436,0.99253,-0.088175,44.777,0.21371,0.10445,0.9713,-73.607,#3,0.97325,0.063094,-0.22092,42.544,-0.08436,0.99253,-0.088175,44.777,0.21371,0.10445,0.9713,-73.607 > view matrix models > #2,0.97325,0.063094,-0.22092,46.993,-0.08436,0.99253,-0.088175,44.775,0.21371,0.10445,0.9713,-80.958,#3,0.97325,0.063094,-0.22092,46.993,-0.08436,0.99253,-0.088175,44.775,0.21371,0.10445,0.9713,-80.958 > clashes #3 restrict #1 name Cl3 1004 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,44.662,-0.08436,0.99253,-0.088175,45.43,0.21371,0.10445,0.9713,-80.336,#3,0.97325,0.063094,-0.22092,44.662,-0.08436,0.99253,-0.088175,45.43,0.21371,0.10445,0.9713,-80.336 > clashes #3 restrict #1 name Cl3 920 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.543,-0.08436,0.99253,-0.088175,46.004,0.21371,0.10445,0.9713,-80.294,#3,0.97325,0.063094,-0.22092,43.543,-0.08436,0.99253,-0.088175,46.004,0.21371,0.10445,0.9713,-80.294 > clashes #3 restrict #1 name Cl3 807 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.439,-0.08436,0.99253,-0.088175,46.524,0.21371,0.10445,0.9713,-80.207,#3,0.97325,0.063094,-0.22092,42.439,-0.08436,0.99253,-0.088175,46.524,0.21371,0.10445,0.9713,-80.207 > clashes #3 restrict #1 name Cl3 754 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.963,-0.08436,0.99253,-0.088175,47.031,0.21371,0.10445,0.9713,-80.45,#3,0.97325,0.063094,-0.22092,41.963,-0.08436,0.99253,-0.088175,47.031,0.21371,0.10445,0.9713,-80.45 > clashes #3 restrict #1 name Cl3 705 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.195,-0.08436,0.99253,-0.088175,46.628,0.21371,0.10445,0.9713,-79.633,#3,0.97325,0.063094,-0.22092,41.195,-0.08436,0.99253,-0.088175,46.628,0.21371,0.10445,0.9713,-79.633 > clashes #3 restrict #1 name Cl3 716 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.284,-0.08436,0.99253,-0.088175,47.078,0.21371,0.10445,0.9713,-80.67,#3,0.97325,0.063094,-0.22092,42.284,-0.08436,0.99253,-0.088175,47.078,0.21371,0.10445,0.9713,-80.67 > clashes #3 restrict #1 name Cl3 698 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.044,-0.08436,0.99253,-0.088175,47.501,0.21371,0.10445,0.9713,-80.958,#3,0.97325,0.063094,-0.22092,42.044,-0.08436,0.99253,-0.088175,47.501,0.21371,0.10445,0.9713,-80.958 > clashes #3 restrict #1 name Cl3 664 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.219,-0.08436,0.99253,-0.088175,47.844,0.21371,0.10445,0.9713,-81.392,#3,0.97325,0.063094,-0.22092,42.219,-0.08436,0.99253,-0.088175,47.844,0.21371,0.10445,0.9713,-81.392 > clashes #3 restrict #1 name Cl3 617 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.471,-0.08436,0.99253,-0.088175,48.603,0.21371,0.10445,0.9713,-82.279,#3,0.97325,0.063094,-0.22092,42.471,-0.08436,0.99253,-0.088175,48.603,0.21371,0.10445,0.9713,-82.279 > clashes #3 restrict #1 name Cl3 552 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.316,-0.08436,0.99253,-0.088175,49.152,0.21371,0.10445,0.9713,-82.738,#3,0.97325,0.063094,-0.22092,42.316,-0.08436,0.99253,-0.088175,49.152,0.21371,0.10445,0.9713,-82.738 > clashes #3 restrict #1 name Cl3 513 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.677,-0.08436,0.99253,-0.088175,49.32,0.21371,0.10445,0.9713,-83.1,#3,0.97325,0.063094,-0.22092,42.677,-0.08436,0.99253,-0.088175,49.32,0.21371,0.10445,0.9713,-83.1 > clashes #3 restrict #1 name Cl3 484 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.159,-0.08436,0.99253,-0.088175,49.696,0.21371,0.10445,0.9713,-83.734,#3,0.97325,0.063094,-0.22092,43.159,-0.08436,0.99253,-0.088175,49.696,0.21371,0.10445,0.9713,-83.734 > clashes #3 restrict #1 name Cl3 448 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.382,-0.08436,0.99253,-0.088175,50.084,0.21371,0.10445,0.9713,-84.239,#3,0.97325,0.063094,-0.22092,43.382,-0.08436,0.99253,-0.088175,50.084,0.21371,0.10445,0.9713,-84.239 > clashes #3 restrict #1 name Cl3 439 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.785,-0.08436,0.99253,-0.088175,50.424,0.21371,0.10445,0.9713,-84.795,#3,0.97325,0.063094,-0.22092,43.785,-0.08436,0.99253,-0.088175,50.424,0.21371,0.10445,0.9713,-84.795 > clashes #3 restrict #1 name Cl3 425 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.204,-0.08436,0.99253,-0.088175,51.066,0.21371,0.10445,0.9713,-85.113,#3,0.97325,0.063094,-0.22092,43.204,-0.08436,0.99253,-0.088175,51.066,0.21371,0.10445,0.9713,-85.113 > clashes #3 restrict #1 name Cl3 468 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.542,-0.08436,0.99253,-0.088175,50.528,0.21371,0.10445,0.9713,-84.765,#3,0.97325,0.063094,-0.22092,43.542,-0.08436,0.99253,-0.088175,50.528,0.21371,0.10445,0.9713,-84.765 > clashes #3 restrict #1 name Cl3 432 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,44.102,-0.08436,0.99253,-0.088175,49.841,0.21371,0.10445,0.9713,-84.391,#3,0.97325,0.063094,-0.22092,44.102,-0.08436,0.99253,-0.088175,49.841,0.21371,0.10445,0.9713,-84.391 > clashes #3 restrict #1 name Cl3 450 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,44.323,-0.08436,0.99253,-0.088175,50.111,0.21371,0.10445,0.9713,-84.778,#3,0.97325,0.063094,-0.22092,44.323,-0.08436,0.99253,-0.088175,50.111,0.21371,0.10445,0.9713,-84.778 > clashes #3 restrict #1 name Cl3 433 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,44.174,-0.08436,0.99253,-0.088175,50.416,0.21371,0.10445,0.9713,-84.998,#3,0.97325,0.063094,-0.22092,44.174,-0.08436,0.99253,-0.088175,50.416,0.21371,0.10445,0.9713,-84.998 > clashes #3 restrict #1 name Cl3 430 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,44.688,-0.08436,0.99253,-0.088175,50.253,0.21371,0.10445,0.9713,-85.118,#3,0.97325,0.063094,-0.22092,44.688,-0.08436,0.99253,-0.088175,50.253,0.21371,0.10445,0.9713,-85.118 > clashes #3 restrict #1 name Cl3 431 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,45.126,-0.08436,0.99253,-0.088175,50.295,0.21371,0.10445,0.9713,-85.397,#3,0.97325,0.063094,-0.22092,45.126,-0.08436,0.99253,-0.088175,50.295,0.21371,0.10445,0.9713,-85.397 > clashes #3 restrict #1 name Cl3 442 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,44.205,-0.08436,0.99253,-0.088175,50.532,0.21371,0.10445,0.9713,-85.13,#3,0.97325,0.063094,-0.22092,44.205,-0.08436,0.99253,-0.088175,50.532,0.21371,0.10445,0.9713,-85.13 > clashes #3 restrict #1 name Cl3 441 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.735,-0.08436,0.99253,-0.088175,50.603,0.21371,0.10445,0.9713,-84.945,#3,0.97325,0.063094,-0.22092,43.735,-0.08436,0.99253,-0.088175,50.603,0.21371,0.10445,0.9713,-84.945 > clashes #3 restrict #1 name Cl3 437 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,43.411,-0.08436,0.99253,-0.088175,51.412,0.21371,0.10445,0.9713,-83.702,#3,0.97325,0.063094,-0.22092,43.411,-0.08436,0.99253,-0.088175,51.412,0.21371,0.10445,0.9713,-83.702 > clashes #3 restrict #1 name Cl3 313 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.972,-0.08436,0.99253,-0.088175,52.333,0.21371,0.10445,0.9713,-82.663,#3,0.97325,0.063094,-0.22092,42.972,-0.08436,0.99253,-0.088175,52.333,0.21371,0.10445,0.9713,-82.663 > clashes #3 restrict #1 name Cl3 230 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.687,-0.08436,0.99253,-0.088175,53.006,0.21371,0.10445,0.9713,-81.708,#3,0.97325,0.063094,-0.22092,42.687,-0.08436,0.99253,-0.088175,53.006,0.21371,0.10445,0.9713,-81.708 > clashes #3 restrict #1 name Cl3 174 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.472,-0.08436,0.99253,-0.088175,53.404,0.21371,0.10445,0.9713,-81.393,#3,0.97325,0.063094,-0.22092,42.472,-0.08436,0.99253,-0.088175,53.404,0.21371,0.10445,0.9713,-81.393 > clashes #3 restrict #1 name Cl3 149 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.986,-0.08436,0.99253,-0.088175,54.165,0.21371,0.10445,0.9713,-81.182,#3,0.97325,0.063094,-0.22092,41.986,-0.08436,0.99253,-0.088175,54.165,0.21371,0.10445,0.9713,-81.182 > clashes #3 restrict #1 name Cl3 123 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.746,-0.08436,0.99253,-0.088175,54.605,0.21371,0.10445,0.9713,-80.848,#3,0.97325,0.063094,-0.22092,41.746,-0.08436,0.99253,-0.088175,54.605,0.21371,0.10445,0.9713,-80.848 > clashes #3 restrict #1 name Cl3 103 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.655,-0.08436,0.99253,-0.088175,54.875,0.21371,0.10445,0.9713,-80.339,#3,0.97325,0.063094,-0.22092,41.655,-0.08436,0.99253,-0.088175,54.875,0.21371,0.10445,0.9713,-80.339 > clashes #3 restrict #1 name Cl3 97 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.349,-0.08436,0.99253,-0.088175,55.458,0.21371,0.10445,0.9713,-79.829,#3,0.97325,0.063094,-0.22092,41.349,-0.08436,0.99253,-0.088175,55.458,0.21371,0.10445,0.9713,-79.829 > clashes #3 restrict #1 name Cl3 95 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.892,-0.08436,0.99253,-0.088175,56.11,0.21371,0.10445,0.9713,-79.866,#3,0.97325,0.063094,-0.22092,40.892,-0.08436,0.99253,-0.088175,56.11,0.21371,0.10445,0.9713,-79.866 > clashes #3 restrict #1 name Cl3 89 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.69,-0.08436,0.99253,-0.088175,56.478,0.21371,0.10445,0.9713,-79.584,#3,0.97325,0.063094,-0.22092,40.69,-0.08436,0.99253,-0.088175,56.478,0.21371,0.10445,0.9713,-79.584 > clashes #3 restrict #1 name Cl3 88 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.263,-0.08436,0.99253,-0.088175,57.105,0.21371,0.10445,0.9713,-79.554,#3,0.97325,0.063094,-0.22092,40.263,-0.08436,0.99253,-0.088175,57.105,0.21371,0.10445,0.9713,-79.554 > clashes #3 restrict #1 name Cl3 91 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.78,-0.08436,0.99253,-0.088175,56.499,0.21371,0.10445,0.9713,-79.032,#3,0.97325,0.063094,-0.22092,40.78,-0.08436,0.99253,-0.088175,56.499,0.21371,0.10445,0.9713,-79.032 > clashes #3 restrict #1 name Cl3 97 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.94,-0.08436,0.99253,-0.088175,56.259,0.21371,0.10445,0.9713,-79.066,#3,0.97325,0.063094,-0.22092,40.94,-0.08436,0.99253,-0.088175,56.259,0.21371,0.10445,0.9713,-79.066 > clashes #3 restrict #1 name Cl3 106 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.66,-0.08436,0.99253,-0.088175,56.748,0.21371,0.10445,0.9713,-78.759,#3,0.97325,0.063094,-0.22092,40.66,-0.08436,0.99253,-0.088175,56.748,0.21371,0.10445,0.9713,-78.759 > clashes #3 restrict #1 name Cl3 96 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.413,-0.08436,0.99253,-0.088175,57.026,0.21371,0.10445,0.9713,-79.051,#3,0.97325,0.063094,-0.22092,40.413,-0.08436,0.99253,-0.088175,57.026,0.21371,0.10445,0.9713,-79.051 > clashes #3 restrict #1 name Cl3 93 clashes > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_basal_89clash.cxs"" > view matrix models > #2,0.97325,0.063094,-0.22092,40.819,-0.08436,0.99253,-0.088175,56.177,0.21371,0.10445,0.9713,-79.387,#3,0.97325,0.063094,-0.22092,40.819,-0.08436,0.99253,-0.088175,56.177,0.21371,0.10445,0.9713,-79.387 > select up 94448 atoms, 95540 bonds, 13 pseudobonds, 5967 residues, 17 models selected > clashes #3 restrict #1 name Cl3 89 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.538,-0.08436,0.99253,-0.088175,55.762,0.21371,0.10445,0.9713,-80.368,#3,0.97325,0.063094,-0.22092,40.538,-0.08436,0.99253,-0.088175,55.762,0.21371,0.10445,0.9713,-80.368 > clashes #3 restrict #1 name Cl3 103 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.433,-0.08436,0.99253,-0.088175,56.611,0.21371,0.10445,0.9713,-79.52,#3,0.97325,0.063094,-0.22092,40.433,-0.08436,0.99253,-0.088175,56.611,0.21371,0.10445,0.9713,-79.52 > clashes #3 restrict #1 name Cl3 96 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.926,-0.08436,0.99253,-0.088175,55.647,0.21371,0.10445,0.9713,-77.706,#3,0.97325,0.063094,-0.22092,42.926,-0.08436,0.99253,-0.088175,55.647,0.21371,0.10445,0.9713,-77.706 > clashes #3 restrict #1 name Cl3 172 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,42.355,-0.08436,0.99253,-0.088175,54.941,0.21371,0.10445,0.9713,-79.173,#3,0.97325,0.063094,-0.22092,42.355,-0.08436,0.99253,-0.088175,54.941,0.21371,0.10445,0.9713,-79.173 > clashes #3 restrict #1 name Cl3 113 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.251,-0.08436,0.99253,-0.088175,55.012,0.21371,0.10445,0.9713,-80.379,#3,0.97325,0.063094,-0.22092,41.251,-0.08436,0.99253,-0.088175,55.012,0.21371,0.10445,0.9713,-80.379 > clashes #3 restrict #1 name Cl3 110 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.826,-0.08436,0.99253,-0.088175,54.68,0.21371,0.10445,0.9713,-81.252,#3,0.97325,0.063094,-0.22092,40.826,-0.08436,0.99253,-0.088175,54.68,0.21371,0.10445,0.9713,-81.252 > clashes #3 restrict #1 name Cl3 126 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.616,-0.08436,0.99253,-0.088175,55.416,0.21371,0.10445,0.9713,-80.662,#3,0.97325,0.063094,-0.22092,40.616,-0.08436,0.99253,-0.088175,55.416,0.21371,0.10445,0.9713,-80.662 > clashes #3 restrict #1 name Cl3 105 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.691,-0.08436,0.99253,-0.088175,53.241,0.21371,0.10445,0.9713,-79.423,#3,0.97325,0.063094,-0.22092,41.691,-0.08436,0.99253,-0.088175,53.241,0.21371,0.10445,0.9713,-79.423 > clashes #3 restrict #1 name Cl3 169 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.439,-0.08436,0.99253,-0.088175,53.437,0.21371,0.10445,0.9713,-80.921,#3,0.97325,0.063094,-0.22092,41.439,-0.08436,0.99253,-0.088175,53.437,0.21371,0.10445,0.9713,-80.921 > clashes #3 restrict #1 name Cl3 164 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.11,-0.08436,0.99253,-0.088175,54.017,0.21371,0.10445,0.9713,-81.835,#3,0.97325,0.063094,-0.22092,41.11,-0.08436,0.99253,-0.088175,54.017,0.21371,0.10445,0.9713,-81.835 > clashes #3 restrict #1 name Cl3 167 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,40.255,-0.08436,0.99253,-0.088175,55.728,0.21371,0.10445,0.9713,-83.564,#3,0.97325,0.063094,-0.22092,40.255,-0.08436,0.99253,-0.088175,55.728,0.21371,0.10445,0.9713,-83.564 > clashes #3 restrict #1 name Cl3 290 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.542,-0.08436,0.99253,-0.088175,52.418,0.21371,0.10445,0.9713,-83.323,#3,0.97325,0.063094,-0.22092,41.542,-0.08436,0.99253,-0.088175,52.418,0.21371,0.10445,0.9713,-83.323 > clashes #3 restrict #1 name Cl3 362 clashes > view matrix models > #2,0.97325,0.063094,-0.22092,41.022,-0.08436,0.99253,-0.088175,53.465,0.21371,0.10445,0.9713,-84.355,#3,0.97325,0.063094,-0.22092,41.022,-0.08436,0.99253,-0.088175,53.465,0.21371,0.10445,0.9713,-84.355 > undo > clashes #3 restrict #1 name Cl3 105 clashes > clashes #3 restrict #1 name Cl3 126 clashes > clashes #3 restrict #1 name Cl3 113 clashes > clashes #3 restrict #1 name Cl3 172 clashes > clashes #3 restrict #1 name Cl3 172 clashes > clashes #3 restrict #1 name Cl3 172 clashes > clashes #3 restrict #1 name Cl3 172 clashes > clashes #3 restrict #1 name Cl3 105 clashes > clashes #3 restrict #1 name Cl3 169 clashes > clashes #3 restrict #1 name Cl3 167 clashes > clashes #3 restrict #1 name Cl3 169 clashes > clashes #3 restrict #1 name Cl3 105 clashes > clashes #3 restrict #1 name Cl3 126 clashes > clashes #3 restrict #1 name Cl3 105 clashes > ui mousemode right select > select clear > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/het_basal_100clash.cxs"" > show #7 models > hide #8 models > hide #7 models > show #8 models > close > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/active Homo > absolute R=0/CaMKII_A_C_blank.cxs"" format session No such file/path: /Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/active Homo absolute R=0/CaMKII_A_C_blank.cxs > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/first run with one > set/inactive_R close #5 > close #6 > show #3 models > hide #3 models > close #3 > color blue, #1/:344-500 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color blue, #1/:344-500 target c Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #1/:344-500 target c, blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color blue #1/:344-500 target c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #1/:344-500 target c Expected an objects specifier or a keyword > select #1/:344-500 Expected an objects specifier or a keyword > hide #!2 models > hide #!4 models > show #!2 models > show #!4 models > select #1/:344-500 atoms Expected an objects specifier or a keyword > select #1/:344- atoms Expected an objects specifier or a keyword > select #1/:344 atoms Expected an objects specifier or a keyword > select #1/A-L:344 atoms Expected a keyword > select #1/A-L:344 atom Expected a keyword > select #1/A-L:344- atoms Expected an objects specifier or a keyword > select #1/A-L:344- atom Expected an objects specifier or a keyword > select #1/A-L:344-end 20279 atoms, 20539 bonds, 10 pseudobonds, 1270 residues, 2 models selected > color sel blue color Missing ""color"" keyword's argument > color sel blue target c > color sel skyblue target c > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homoBASAL30.pb"" Line 0 ""#3/A:245@CA #2/c:317@CA "", got 0 atoms for spec ""#3/A:245@CA"", require exactly 1 > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homoBASAL30.pb"" Opened Pseudobonds homoBASAL30.pb, 136 bonds > save /Users/Andrew/Desktop/image12.png supersample 3 > close #3 > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homoBASAL30_same.pb"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 457, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/read_pbonds/__init__.py"", line 25, in open return readpbonds.read_pseudobond_file(session, data, file_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/read_pbonds/readpbonds.py"", line 55, in read_pseudobond_file b = g.new_pseudobond(a1[0], a2[0]) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 447, in new_pseudobond pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer) TypeError: Can't form pseudobond to itself Populating font family aliases took 375 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. TypeError: Can't form pseudobond to itself File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 447, in new_pseudobond pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer) See log for complete Python traceback. > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homoBASAL30_same.pb"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 457, in collated_open return remember_data_format() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/read_pbonds/__init__.py"", line 25, in open return readpbonds.read_pseudobond_file(session, data, file_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/read_pbonds/readpbonds.py"", line 55, in read_pseudobond_file b = g.new_pseudobond(a1[0], a2[0]) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 447, in new_pseudobond pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer) TypeError: Can't form pseudobond to itself TypeError: Can't form pseudobond to itself File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 447, in new_pseudobond pb = f(self._c_pointer, atom1._c_pointer, atom2._c_pointer) See log for complete Python traceback. > open ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homoBASAL30_same.pb"" Opened Pseudobonds homoBASAL30_same.pb, 128 bonds Drag select of 6 pseudobonds > select clear > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homobasal30_same.cxs"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 543, in include_state return bool(self.group_map) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 536, in group_map f = c_function('set_pbgroup_py_instance', File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 31, in c_function f = getattr(self._c_lib, func_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 387, in __getattr__ func = self.__getitem__(name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 543, in include_state return bool(self.group_map) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 536, in group_map f = c_function('set_pbgroup_py_instance', File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 31, in c_function f = getattr(self._c_lib, func_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 387, in __getattr__ func = self.__getitem__(name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) See log for complete Python traceback. > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homoBASAL30Same.cxs"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 543, in include_state return bool(self.group_map) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 536, in group_map f = c_function('set_pbgroup_py_instance', File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 31, in c_function f = getattr(self._c_lib, func_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 387, in __getattr__ func = self.__getitem__(name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 543, in include_state return bool(self.group_map) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 536, in group_map f = c_function('set_pbgroup_py_instance', File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 31, in c_function f = getattr(self._c_lib, func_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 387, in __getattr__ func = self.__getitem__(name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found AttributeError: dlsym(0x21a5cda60, set_pbgroup_py_instance): symbol not found File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py"", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) See log for complete Python traceback. > close #3 > save ""/Users/Andrew/Nextcloud/CaMKII/modelling crosslinks/2nd > analyses/homo_model.cxs"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 249, in discovery if hasattr(sm, 'include_state') and not sm.include_state(value): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 247, in include_state self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/attributes.py"", line 247, in self._python_instances = [[inst for inst in inst_func(self.session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/structure.py"", line 2481, in register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls), File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in python_instances_of_class return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 49, in return [x for x in instances if filt(x)] File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 44, in filt = lambda x: (not x.group.structure) or x.group.structure.id File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 100, in get_prop return astype(v.value) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/ctypes_support.py"", line 69, in pseudobond_group return PseudobondGroupData.c_ptr_to_py_inst(p) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 2297, in args = (ctypes.c_void_p,), ret = ctypes.py_object)(ctypes.c_void_p(int(ptr))) TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType' TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molobject.py"", line 2297, in args = (ctypes.c_void_p,), ret = ctypes.py_object)(ctypes.c_void_p(int(ptr))) See log for complete Python traceback. ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 19 days 18:29 Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 et-xmlfile: 1.1.0 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openpyxl: 3.0.10 openvr: 1.16.802 packaging: 21.0 pandas: 1.4.3 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 QtRangeSlider: 0.1.5 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 seaborn: 0.11.2 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect feedback normal Input/Output Tom Goddard all ChimeraX