id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6035 OpenGL out of memory error, then crash several commands later on Windows chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22000 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x00001948 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 576 in _handle_results File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006d74 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 528 in _handle_tasks File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00004e1c (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py"", line 816 in _exhaustive_wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py"", line 884 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 499 in _wait_for_updates File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 519 in _handle_workers File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006dd4 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00005f7c (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002d84 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000064b0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000050c0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00004a34 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00005340 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00003808 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00007654 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000051e0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002710 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00004208 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in 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call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py"", line 816 in _exhaustive_wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py"", line 884 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 499 in _wait_for_updates File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 519 in _handle_workers File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00004490 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000065d8 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00005ff4 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002b14 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program 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_bootstrap Thread 0x00004ab0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00007674 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000036d4 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00004b4c (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006048 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00001be8 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006b14 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 576 in _handle_results File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00005744 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 528 in _handle_tasks File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00005e14 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py"", line 816 in _exhaustive_wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py"", line 884 in wait File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 499 in _wait_for_updates File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 519 in _handle_workers File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00001c50 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00000a50 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000035cc (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000043c0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00005520 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006258 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006494 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006304 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000064c0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x0000376c (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002fcc (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006508 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00000e60 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py"", line 576 in _handle_results File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00006d70 (most recent call first): File ""C:\Program Files\ChimeraX 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""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3\bin\lib\threading.py"", line 930 in _bootstrap ... ===== Log before crash start ===== UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\Users\lilyh\Downloads\job866_VF_postprocess_5.06A (1).mrc"" format > mrc Opened job866_VF_postprocess_5.06A (1).mrc as #1, grid size 400,400,400, pixel 1.05, shown at level 0.00336, step 2, values float32 > volume #1 step 1 > volume #1 level 0.01122 > volume #1 level 0.008029 > open ""C:/Users/lilyh/Downloads/AF into EM version 3 (4).cxs"" Error opening map ""C:\Users\lilyh\Downloads\AF into EM version 3 (4).cxs"": File AF into EM version 3 (4).cxs, format mrc MRC header value nsymbt (1701082415) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Error opening map ""C:\Users\lilyh\Downloads\AF into EM version 3 (4).cxs"": File AF into EM version 3 (4).cxs, format mrc MRC header value nsymbt (1701082415) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None opened ChimeraX session > open ""C:/Users/lilyh/Downloads/job862_Kinase_postprocess_6.7A (1).mrc"" Opened job862_Kinase_postprocess_6.7A (1).mrc as #1, grid size 400,400,400, pixel 1.05, shown at level 0.00103, step 2, values float32 > open ""C:/Users/lilyh/Downloads/job866_VF_postprocess_5.06A (1).mrc"" Opened job866_VF_postprocess_5.06A (1).mrc as #2, grid size 400,400,400, pixel 1.05, shown at level 0.00336, step 2, values float32 > hide #3.4 models > show #3.4 models > hide #3.1 models > hide #3.2 models > hide #3.3 models > hide #3.4 models > hide #3.5 models > hide #!4 models > hide #5 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!1 models > close #1 > volume #2 step 1 > volume #2 level 0.0118 > volume #2 level 0.01135 > volume gaussian #2 sdev2 Expected a keyword > volume gaussian #2 sDev 2 Opened job866_VF_postprocess_5.06A (1).mrc gaussian as #1, grid size 400,400,400, pixel 1.05, shown at step 1, values float32 > volume #1 level 0.002588 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > ui tool show AlphaFold > close #2 > alphafold search #3.1 ChimeraX REST job id: EEYTV4OQAHMC0V05OX5PY1GIU9CPC2LBHHGRU2XY6RBRXC1U0GT14D3IB7KP63T6 > alphafold search #3.1 ChimeraX REST job id: HRCLWYDRNPBJY6SPIRQTW8QSUAYQ9GBDEY55Y8CDXTKHLCNSL2E0CXQAP8BAU26N BlastProtein finished. Parsing BLAST results. > alphafold match #3.1 1 AlphaFold model found using UniProt identifier: Q08AM6 (chain A) AlphaFold chains matching AF_hsVac14_pentamer.pdb --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | VAC14_HUMAN | Q08AM6 | 0.00 | 782 | 782 | 100 Opened 1 AlphaFold model BlastProtein finished. Parsing BLAST results. > alphafold search #3.2 ChimeraX REST job id: G32F5HWLS6Z8255U2HVK9QGJYEE9J56R25Y0ST6S1LGEVL07VK4YX1X8WZM3GV7O > alphafold search #3.2 ChimeraX REST job id: LL290JDJKBJHHF7CK2295O8JI36H4XMTU4BYMJFRGA35VOI0K6KAMG5290WHERM1 BlastProtein finished. Parsing BLAST results. BlastProtein finished. Parsing BLAST results. > alphafold fetch VAC14_YEAST alignTo #3.2/A AlphaFold chains matching chain A --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | VAC14_YEAST | Q06708 | 7.20 | 871 | 782 | 34 > matchmaker #6 to #3.2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF_hsVac14_pentamer.pdb, chain A (#3.2) with AlphaFold VAC14_YEAST, chain A (#6), sequence alignment score = 1528.7 RMSD between 338 pruned atom pairs is 1.146 angstroms; (across all 657 pairs: 7.247) > ui tool show AlphaFold > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > close #2.1 > ui tool show AlphaFold > show #3.1 models > hide #3.1 models > alphafold search #3.1 ChimeraX REST job id: 81T1OTFHUJPFJ9YA9CVMYHW5N3E4YQIKJ0W6WPK96H6OGTDB8X9JF7LDBM08SCD6 > alphafold search #3.1 ChimeraX REST job id: M6GU5VD269WIIFIRC55PC6XQ5L1ZLXMG4WN53DBUQTMT9ND89MBF2PZYQFC7HIFB BlastProtein finished. Parsing BLAST results. BlastProtein finished. Parsing BLAST results. > alphafold match #3.1 1 AlphaFold model found using UniProt identifier: Q08AM6 (chain A) AlphaFold chains matching AF_hsVac14_pentamer.pdb --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | VAC14_HUMAN | Q08AM6 | 0.00 | 782 | 782 | 100 Opened 1 AlphaFold model > alphafold fetch VAC14_YEAST alignTo #3.1/A AlphaFold chains matching chain A --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | VAC14_YEAST | Q06708 | 7.20 | 871 | 782 | 34 > matchmaker #8 to #3.1/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF_hsVac14_pentamer.pdb, chain A (#3.1) with AlphaFold VAC14_YEAST, chain A (#8), sequence alignment score = 1528.7 RMSD between 338 pruned atom pairs is 1.146 angstroms; (across all 657 pairs: 7.247) > close #7.1 > hide #8 models > show #8 models > hide #8 models > show #8 models > show #!4 models > hide #!4 models > alphafold search #4 ChimeraX REST job id: 3WDLDVD8RGSTGAUEV5X3AM03803HFUJ7XAJB532C8EKGFR5K5495VS9HZAX21YC1 > alphafold search #4 ChimeraX REST job id: FPGR82IMZ8XHZIXQS4VJRBKO0BZJEWFXY973I43BEZYUKFAEMYKNB4G50TSJ1CTJ BlastProtein finished. Parsing BLAST results. BlastProtein finished. Parsing BLAST results. > show #!4 models > hide #!4 models > alphafold fetch FAB1_YEAST alignTo #4/A Fetching compressed AlphaFold P34756 from https://alphafold.ebi.ac.uk/files/AF-P34756-F1-model_v1.cif AlphaFold chains matching chain A --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | FAB1_YEAST | P34756 | 25.73 | 1698 | 1279 | 28 > matchmaker #9 to #4/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Alphafold_domain_colored.pdb, chain A (#4) with AlphaFold FAB1_YEAST, chain A (#9), sequence alignment score = 1869.8 RMSD between 460 pruned atom pairs is 1.185 angstroms; (across all 1171 pairs: 25.734) > alphafold search #5 ChimeraX REST job id: TEASL6PF0X4SZNNVLE7GIWAUABF5PX8F70S1IUVYE4JP9HPUIMEB18DTE2NX24K3 > alphafold search #5 ChimeraX REST job id: NJBQAOJ8VZG11LRT6558HPEX3DQSRM40DEETOATQN2ZA8CSKWOG7UM27SLQFBRBY > alphafold search #5 ChimeraX REST job id: K85Y678G0BD8LA2JX35DLRKE1NU6R5TMZCUX8Q7QGVRO7V8GUNLFCRLYWCKRN8SW BlastProtein finished. Parsing BLAST results. > close #1 BlastProtein finished. Parsing BLAST results. BlastProtein finished. Parsing BLAST results. > alphafold fetch FIG4_YEAST alignTo #5/A Fetching compressed AlphaFold P42837 from https://alphafold.ebi.ac.uk/files/AF-P42837-F1-model_v1.cif AlphaFold chains matching chain A --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | FIG4_YEAST | P42837 | 29.33 | 865 | 907 | 38 > matchmaker #1 to #5/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Alpha_fold_Fig4.pdb, chain A (#5) with AlphaFold FIG4_YEAST, chain A (#1), sequence alignment score = 1724.7 RMSD between 512 pruned atom pairs is 0.821 angstroms; (across all 793 pairs: 29.327) > ui tool show ""Volume Viewer"" > close #1 > hide #!3 models > show #!3 models > hide #7 models > show #7 models > hide #8 models > show #8 models > show #!4 models > hide #!4 models > hide #2 models > show #2 models > hide #!3 models > show #!3 models > hide #2 models > show #2 models > open ""C:/Users/lilyh/Downloads/job862_Kinase_postprocess_6.7A (1).mrc"" Opened job862_Kinase_postprocess_6.7A (1).mrc as #1, grid size 400,400,400, pixel 1.05, shown at level 0.00103, step 2, values float32 > open ""C:/Users/lilyh/Downloads/job866_VF_postprocess_5.06A (1).mrc"" Opened job866_VF_postprocess_5.06A (1).mrc as #10, grid size 400,400,400, pixel 1.05, shown at level 0.00336, step 2, values float32 > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!1 models > show #!1 models > hide #2 models > show #2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #10 step 1 > volume #10 level 0.007419 > volume gaussian #10 sDev 2 Opened job866_VF_postprocess_5.06A (1).mrc gaussian as #11, grid size 400,400,400, pixel 1.05, shown at step 1, values float32 > volume #11 level 0.002197 > hide #6 models > show #6 models > hide #9 models > show #9 models > hide #9 models > hide #8 models > hide #!11 models > show #!11 models > hide #6 models > show #6 models > ui mousemode right ""translate selected models"" Drag select of 5 residues > ui mousemode right ""translate selected models"" > ui mousemode right select > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right select > ui mousemode right translate > select #6 6944 atoms, 7061 bonds, 871 residues, 1 model selected > ~select #6 Nothing selected > select #6 6944 atoms, 7061 bonds, 871 residues, 1 model selected > ui mousemode right ""translate selected models"" > hide #6 models > show #6 models > ~select #6 Nothing selected > select #6 6944 atoms, 7061 bonds, 871 residues, 1 model selected > hide #!11 models > ui mousemode right select > ui mousemode right ""translate selected models"" > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #6 models > hide #7 models > show #7 models > show #6 models > ui mousemode right select > hide #!11 target m > ui mousemode right ""translate selected models"" > ui mousemode right translate > ui mousemode right ""move picked models"" > show #!11 models > view matrix models > #6,-0.21159,0.77628,0.59381,298.24,0.86772,0.42881,-0.25138,166.37,-0.44977,0.46207,-0.76432,385.15 > view matrix models > #6,-0.21159,0.77628,0.59381,293.19,0.86772,0.42881,-0.25138,169.68,-0.44977,0.46207,-0.76432,377.06 > volume #11 level 0.004047 > volume #11 level 0.007747 > view matrix models > #6,-0.21159,0.77628,0.59381,294.68,0.86772,0.42881,-0.25138,194.76,-0.44977,0.46207,-0.76432,293.76 > view matrix models #11,1,0,0,5.331,0,1,0,-0.67759,0,0,1,11.814 > view matrix models #11,1,0,0,8.4687,0,1,0,1.1294,0,0,1,21.46 > view matrix models #11,1,0,0,8.5854,0,1,0,-2.0235,0,0,1,17.271 > view matrix models > #6,-0.21159,0.77628,0.59381,303.34,0.86772,0.42881,-0.25138,185.84,-0.44977,0.46207,-0.76432,296.75 > view matrix models > #6,-0.21159,0.77628,0.59381,303.22,0.86772,0.42881,-0.25138,182.24,-0.44977,0.46207,-0.76432,309.07 > view matrix models > #6,-0.21159,0.77628,0.59381,303.56,0.86772,0.42881,-0.25138,182.27,-0.44977,0.46207,-0.76432,309.55 > view matrix models > #6,-0.21159,0.77628,0.59381,292.62,0.86772,0.42881,-0.25138,182.48,-0.44977,0.46207,-0.76432,295.16 > view matrix models > #6,-0.21159,0.77628,0.59381,293.21,0.86772,0.42881,-0.25138,179.82,-0.44977,0.46207,-0.76432,293.02 > ui tool show ""Fit in Map"" Fit molecule AlphaFold VAC14_YEAST (#6) to map job866_VF_postprocess_5.06A (1).mrc gaussian (#11) using 6944 atoms average map value = 0.005491, steps = 140 shifted from previous position = 23.3 rotated from previous position = 0.807 degrees atoms outside contour = 4575, contour level = 0.007747 Position of AlphaFold VAC14_YEAST (#6) relative to job866_VF_postprocess_5.06A (1).mrc gaussian (#11) coordinates: Matrix rotation and translation -0.21430801 0.76746845 0.60420548 267.83064670 0.86687911 0.43448951 -0.24441661 170.09255725 -0.45010298 0.47139267 -0.75841694 286.96897086 Axis 0.56000727 0.82482920 0.07777308 Axis point 133.69328583 0.00000000 115.14967302 Rotation angle (degrees) 140.27472700 Shift along axis 312.60287729 > show #8 models > ~select #6 Nothing selected > select #8 6944 atoms, 7061 bonds, 871 residues, 1 model selected > view matrix models > #8,-0.55035,0.53567,0.64045,254.9,0.34623,0.84442,-0.40876,169.55,-0.75977,-0.0032144,-0.65019,245.59 > view matrix models > #8,-0.55035,0.53567,0.64045,252.18,0.34623,0.84442,-0.40876,172.28,-0.75977,-0.0032144,-0.65019,245.53 > view matrix models > #8,-0.55035,0.53567,0.64045,252.37,0.34623,0.84442,-0.40876,171.45,-0.75977,-0.0032144,-0.65019,251.23 > view matrix models #11,1,0,0,27.938,0,1,0,3.5697,0,0,1,41.683 > view matrix models #11,1,0,0,26.814,0,1,0,4.1647,0,0,1,41.473 > view matrix models #11,1,0,0,34.197,0,1,0,6.6495,0,0,1,51.248 > view matrix models #11,1,0,0,9.2691,0,1,0,-1.4344,0,0,1,14.129 > view matrix models > #8,-0.55035,0.53567,0.64045,251.97,0.34623,0.84442,-0.40876,171.73,-0.75977,-0.0032144,-0.65019,251.22 > view matrix models > #8,-0.55035,0.53567,0.64045,245.35,0.34623,0.84442,-0.40876,161.82,-0.75977,-0.0032144,-0.65019,246.13 > view matrix models > #8,-0.55035,0.53567,0.64045,246.63,0.34623,0.84442,-0.40876,163.87,-0.75977,-0.0032144,-0.65019,245.25 > view matrix models > #8,-0.55035,0.53567,0.64045,246.63,0.34623,0.84442,-0.40876,163.02,-0.75977,-0.0032144,-0.65019,245 Fit molecule AlphaFold VAC14_YEAST (#8) to map job866_VF_postprocess_5.06A (1).mrc gaussian (#11) using 6944 atoms average map value = 0.005715, steps = 68 shifted from previous position = 1.98 rotated from previous position = 1.11 degrees atoms outside contour = 4609, contour level = 0.007747 Position of AlphaFold VAC14_YEAST (#8) relative to job866_VF_postprocess_5.06A (1).mrc gaussian (#11) coordinates: Matrix rotation and translation -0.54789186 0.53111740 0.64631943 237.72700904 0.32974655 0.84716282 -0.41663217 165.29505458 -0.76881839 -0.01514777 -0.63928775 229.08503023 Axis 0.27041321 0.95314280 -0.13563002 Axis point 154.86876254 0.00000000 82.89718290 Rotation angle (degrees) 132.06771271 Shift along axis 190.76350597 > show #!10 models > hide #!10 models > show #5 models > hide #5 models > show #!10 models > hide #!10 models > show #5 models > hide #5 models > ui tool show AlphaFold > alphafold search #5 ChimeraX REST job id: GIKVIOOEFQEXO3PP7PDRNDX9WZ1M1JKH7ZO66L9SKSO4Z6OJOUSZU6E92NLT2WA2 BlastProtein finished. QWindowsWindow::setGeometry: Unable to set geometry 2256x1516+0+34 (frame: 2278x1572-11-11) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 2256x1398+0+34 (frame: 2278x1454-11-11) margins: 11, 45, 11, 11 minimum size: 564x758 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1150,1572 maxtrack=0,0) Parsing BLAST results. QWindowsWindow::setGeometry: Unable to set geometry 2256x1748+0+34 (frame: 2278x1804-11-11) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 2256x1398+0+34 (frame: 2278x1454-11-11) margins: 11, 45, 11, 11 minimum size: 564x874 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1150,1804 maxtrack=0,0) > alphafold fetch FIG4_YEAST alignTo #5/A AlphaFold chains matching chain A --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id A | FIG4_YEAST | P42837 | 29.33 | 865 | 907 | 38 > matchmaker #12 to #5/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Alpha_fold_Fig4.pdb, chain A (#5) with AlphaFold FIG4_YEAST, chain A (#12), sequence alignment score = 1724.7 RMSD between 512 pruned atom pairs is 0.821 angstroms; (across all 793 pairs: 29.327) > select clear > hide #6 models > hide #12 models > show #12 models > hide #8 models > volume #11 level 0.01073 > volume #11 level 0.007804 > volume #11 level 0.006773 Drag select of 3 residues > ui mousemode right select > show #5 models > hide #5 models > show #5 models > hide #5 models > show #!10 models > hide #!10 models > hide #12 models > show #12 models > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.9933,0.10138,-0.055508,223.52,-0.11536,-0.89933,0.42179,196.32,-0.007157,0.42536,0.90499,272.56 > view matrix models > #12,-0.9933,0.10138,-0.055508,220.08,-0.11536,-0.89933,0.42179,196.65,-0.007157,0.42536,0.90499,278.16 > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.94943,0.010447,-0.31381,224.78,-0.12785,-0.92571,0.35598,197.42,-0.28678,0.37809,0.88023,273.45 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.94943,0.010447,-0.31381,220.75,-0.12785,-0.92571,0.35598,198.02,-0.28678,0.37809,0.88023,278.77 > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.95282,-0.011709,-0.30331,220.62,-0.10954,-0.91865,0.37958,198.01,-0.28308,0.3949,0.87403,278.86 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.97518,0.22113,-0.010927,215.34,-0.2043,-0.87973,0.42935,195.41,0.085332,0.42093,0.90307,285.26 > view matrix models > #12,-0.95363,-0.18334,-0.23869,220.34,0.023843,-0.83658,0.54733,197.9,-0.30003,0.51626,0.80216,279.09 > view matrix models > #12,-0.90923,-0.045544,-0.41379,223.08,-0.099231,-0.94163,0.32168,199.08,-0.40429,0.33354,0.85164,277.12 > view matrix models > #12,-0.92528,-0.030474,-0.37806,222.23,-0.13664,-0.90306,0.40721,197.07,-0.35382,0.42844,0.83142,278 > view matrix models > #12,-0.90955,-0.08779,-0.40623,223.12,-0.035779,-0.95727,0.28698,200.8,-0.41406,0.27556,0.86754,276.93 > view matrix models > #12,-0.88905,0.059923,-0.45387,223.62,-0.24222,-0.90284,0.35526,195.81,-0.38849,0.42578,0.81718,277.56 > view matrix models > #12,-0.87503,0.14639,-0.4614,223.68,-0.25109,-0.95218,0.17409,198.31,-0.41385,0.26818,0.86995,276.93 > view matrix models > #12,-0.92946,0.055652,-0.36471,221.66,-0.18828,-0.92168,0.33919,197.1,-0.31727,0.38393,0.86714,278.35 > view matrix models > #12,-0.94841,0.09883,-0.30124,220.28,-0.19405,-0.93236,0.30504,197.5,-0.25072,0.34776,0.90344,279.23 > view matrix models > #12,-0.94933,0.10074,-0.29768,220.2,-0.19672,-0.92919,0.31289,197.33,-0.24509,0.3556,0.90193,279.33 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.94933,0.10074,-0.29768,217.62,-0.19672,-0.92919,0.31289,198.31,-0.24509,0.3556,0.90193,279.86 Fit molecule AlphaFold FIG4_YEAST (#12) to map job866_VF_postprocess_5.06A (1).mrc gaussian (#11) using 7077 atoms average map value = 0.005856, steps = 276 shifted from previous position = 25.5 rotated from previous position = 16.2 degrees atoms outside contour = 3914, contour level = 0.0067731 Position of AlphaFold FIG4_YEAST (#12) relative to job866_VF_postprocess_5.06A (1).mrc gaussian (#11) coordinates: Matrix rotation and translation -0.99520086 0.08947529 -0.03961597 228.42910668 -0.09782440 -0.89990208 0.42497839 193.70549892 0.00237457 0.42681427 0.90433619 279.00387751 Axis 0.00956397 -0.21874895 -0.97573430 Axis point 118.67192851 59.87389633 0.00000000 Rotation angle (degrees) 174.49233922 Shift along axis -312.42183870 > volume #11 level 0.006945 > show #!10 models > hide #!10 models > show #5 models > hide #5 models > show #5 models > hide #5 models > select clear > show #6 models > hide #6 models > show #6 models > hide #6 models > show #!10 models > hide #!10 models > show #9 models > hide #9 models > show #9 models > show #!10 models > hide #!10 models > hide #9 models > show #9 models > show #!4 models > hide #!4 models > show #!1 models > volume #1 level 0.008162 > hide #!11 models > show #!11 models > volume #1 level 0.006814 > volume #1 level 0.005272 > volume #1 level 0.004887 > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > volume #1 level 0.01192 > volume #1 level 0.007199 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.005176 > volume #1 level 0.008066 > ui mousemode right select > select #9/A:1026 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.86715,-0.249,0.43134,198.38,-0.12952,0.72351,0.67805,240.28,-0.48092,-0.64384,0.59514,185.11 > view matrix models > #9,0.86346,0.14301,0.48371,196.91,-0.49691,0.076456,0.86443,234.77,0.086642,-0.98676,0.13708,198.4 > view matrix models > #9,-0.25748,-0.25146,-0.93299,187.57,-0.9502,0.24133,0.19719,230.65,0.17557,0.9373,-0.30108,197.16 > view matrix models > #9,-0.11805,-0.9673,-0.22449,187.68,-0.57262,-0.11838,0.81123,234.35,-0.81127,0.22431,-0.53992,183.91 > view matrix models > #9,-0.10604,-0.9271,-0.3595,188.58,-0.64945,-0.2092,0.73106,233.79,-0.75298,0.311,-0.57992,184.89 > ui mousemode right ""translate selected models"" > view matrix models > #9,-0.10604,-0.9271,-0.3595,163.68,-0.64945,-0.2092,0.73106,248.58,-0.75298,0.311,-0.57992,249.92 > view matrix models > #9,-0.10604,-0.9271,-0.3595,162.21,-0.64945,-0.2092,0.73106,245.41,-0.75298,0.311,-0.57992,259.8 > view matrix models > #9,-0.10604,-0.9271,-0.3595,206.16,-0.64945,-0.2092,0.73106,216.07,-0.75298,0.311,-0.57992,149.86 > view matrix models > #9,-0.10604,-0.9271,-0.3595,207.73,-0.64945,-0.2092,0.73106,213.83,-0.75298,0.311,-0.57992,154.8 > ui mousemode right ""rotate selected models"" > view matrix models > #9,-0.11417,-0.92547,-0.3612,207.6,-0.63212,-0.21281,0.74507,214.04,-0.76641,0.31339,-0.56072,154.45 > view matrix models > #9,0.78455,-0.51279,0.3486,217.37,-0.5589,-0.34135,0.75572,215.58,-0.26853,-0.78774,-0.5544,165.9 > view matrix models > #9,0.69548,-0.63015,0.34529,216.21,-0.44049,0.0057561,0.89774,215.76,-0.5677,-0.77645,-0.27357,159.13 > view matrix models > #9,0.83426,-0.50317,0.22544,218.92,-0.25679,0.007248,0.96644,218.44,-0.48792,-0.86416,-0.12316,159.82 > view matrix models > #9,0.86936,-0.20784,0.44835,217.35,-0.46894,-0.63318,0.61578,218.75,0.1559,-0.74558,-0.64792,173.51 > view matrix models > #9,0.68006,-0.55483,0.47925,214.94,-0.30534,0.37996,0.87316,217.14,-0.66655,-0.74013,0.088983,155.19 > view matrix models > #9,0.85553,0.49435,-0.1539,218.77,-0.33624,0.75652,0.56091,217.44,0.39371,-0.42813,0.81345,167.88 > view matrix models > #9,0.93906,0.29531,-0.17597,220.87,-0.16277,0.83283,0.52905,220.35,0.30278,-0.46817,0.83015,166.36 > view matrix models > #9,0.87383,0.34559,-0.34203,220.62,0.10795,0.54799,0.82949,223.91,0.4741,-0.76176,0.44154,172.4 > view matrix models > #9,0.98722,0.1571,0.026584,220.85,-0.086533,0.38854,0.91736,220.55,0.13379,-0.90794,0.39717,167.33 > view matrix models > #9,0.98524,0.17078,0.011701,220.87,-0.070228,0.34092,0.93747,220.84,0.15611,-0.92445,0.34788,168.05 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.98524,0.17078,0.011701,214.55,-0.070228,0.34092,0.93747,252.4,0.15611,-0.92445,0.34788,195.95 > view matrix models > #9,0.98524,0.17078,0.011701,215.98,-0.070228,0.34092,0.93747,248.66,0.15611,-0.92445,0.34788,196.84 > view matrix models > #9,0.98524,0.17078,0.011701,217.11,-0.070228,0.34092,0.93747,243.8,0.15611,-0.92445,0.34788,193.56 > view matrix models > #9,0.98524,0.17078,0.011701,214.32,-0.070228,0.34092,0.93747,249.07,0.15611,-0.92445,0.34788,187.5 > view matrix models > #9,0.98524,0.17078,0.011701,217.03,-0.070228,0.34092,0.93747,244.95,0.15611,-0.92445,0.34788,195.49 > view matrix models > #9,0.98524,0.17078,0.011701,215.96,-0.070228,0.34092,0.93747,247.11,0.15611,-0.92445,0.34788,193.43 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.95691,0.16642,0.23798,214.13,-0.27412,0.24715,0.9294,243.98,0.095857,-0.95458,0.28212,192.89 > view matrix models > #9,0.95477,0.22317,0.1965,214.19,-0.21753,0.073684,0.97327,245.15,0.20272,-0.97199,0.1189,195.72 > view matrix models > #9,0.97735,0.1846,0.1035,215.23,-0.14621,0.23536,0.96085,245.98,0.15302,-0.95422,0.25702,194 > view matrix models > #9,0.97572,-0.19264,0.10417,216.26,-0.049703,0.26847,0.962,247.51,-0.21329,-0.94383,0.25238,187.82 > view matrix models > #9,0.98771,-0.14115,0.067081,216.54,-0.053323,0.099099,0.99365,247.74,-0.1469,-0.98502,0.090355,190.02 > view matrix models > #9,0.9811,-0.073636,0.17892,215.57,-0.15201,0.27873,0.94826,245.84,-0.1197,-0.95754,0.26227,189.38 > view matrix models > #9,0.9907,-0.011868,0.13556,215.82,-0.13419,0.080384,0.98769,246.46,-0.022619,-0.99669,0.078044,192.23 > hide #9 models > show #9 models > hide #9 models > show #9 models Fit molecule AlphaFold FAB1_YEAST (#9) to map job862_Kinase_postprocess_6.7A (1).mrc (#1) using 13607 atoms average map value = 0.003648, steps = 212 shifted from previous position = 17.8 rotated from previous position = 19.1 degrees atoms outside contour = 10319, contour level = 0.008066 Position of AlphaFold FAB1_YEAST (#9) relative to job862_Kinase_postprocess_6.7A (1).mrc (#1) coordinates: Matrix rotation and translation 0.89270911 0.01315092 0.45044149 197.93009494 -0.45046926 0.05302122 0.89121617 235.30744014 -0.01216265 -0.99850681 0.05325661 196.90289384 Axis -0.94486158 0.23130209 -0.23181011 Axis point 0.00000000 224.17165919 -72.08961071 Rotation angle (degrees) 90.02902181 Shift along axis -178.23352185 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!11 models > show #!11 models > hide #!4 models > show #8 models > hide #8 models > show #!4 models > hide #!4 models > show #5 models > hide #5 models > show #!4 models > hide #!4 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #8 models > hide #8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > select #6/A:37 12 atoms, 12 bonds, 1 residue, 1 model selected > select #6/A:37-154 925 atoms, 939 bonds, 118 residues, 1 model selected > select #6/A:10-17 72 atoms, 72 bonds, 8 residues, 1 model selected > show #6 models > select #6/A:75-76 12 atoms, 11 bonds, 2 residues, 1 model selected > select #6/A:75-201 995 atoms, 1010 bonds, 127 residues, 1 model selected > hide #6 models > show #6 models > hide #6 models > show #6 models > select #6/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!11 models > view matrix models > #6,-0.64877,0.76097,-0.0057184,278.71,0.63474,0.53698,-0.55566,168.3,-0.41976,-0.36412,-0.83139,311.91 > show #!11 models Fit molecule AlphaFold VAC14_YEAST (#6) to map job866_VF_postprocess_5.06A (1).mrc gaussian (#11) using 6944 atoms average map value = 0.005491, steps = 408 shifted from previous position = 8.22 rotated from previous position = 49.8 degrees atoms outside contour = 4172, contour level = 0.006945 Position of AlphaFold VAC14_YEAST (#6) relative to job866_VF_postprocess_5.06A (1).mrc gaussian (#11) coordinates: Matrix rotation and translation -0.21659920 0.76814311 0.60252879 267.79415073 0.86583992 0.43626924 -0.24492935 170.07118000 -0.45100557 0.46864198 -0.75958454 286.96542047 Axis 0.55914150 0.82553035 0.07655344 Axis point 133.74431916 0.00000000 115.22805955 Rotation angle (degrees) 140.35004968 Shift along axis 312.10193260 > select #6/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!11 models > ui mousemode right translate > ui mousemode right zoom > ui mousemode right ""translate selected models"" > select #6/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > ui tool show Contacts > contacts sel resSeparation 3 133 contacts > contacts sel resSeparation 3 133 contacts > contacts sel resSeparation 3 133 contacts > hide #13 models > show #13 models > hide #12 models > show #12 models > show sel atoms Drag select of 1 residues > show sel atoms > select clear Drag select of 2 atoms, 1 residues > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #12/A Alignment identifier is 12/A Drag select of 1 residues > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > hide #12 models > show #12 models > ui tool show Contacts > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > select #6/A:10-11 14 atoms, 13 bonds, 2 residues, 1 model selected > select #6/A:10-18 81 atoms, 81 bonds, 9 residues, 1 model selected > select clear > select #6/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #6/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > show #8 models > ui tool show ""Show Sequence Viewer"" > hide #6 models > show #6 models > sequence chain #8/A Alignment identifier is 8/A > select #8/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > show #!11 models > hide #!11 models > select #8/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:59-60 13 atoms, 12 bonds, 2 residues, 1 model selected > select #8/A:59-60 13 atoms, 12 bonds, 2 residues, 1 model selected > select #8/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > hide #12 models > show #12 models > hide #12 models > select #8/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel magenta > show sel atoms > select #8/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel magenta > select #8/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel magenta > select clear > select #8/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel white > show sel atoms Drag select of 1 atoms, 2 residues > select clear Drag select of 1 atoms, 2 residues > select clear Drag select of 1 atoms, 2 residues > color sel white > select clear > show #12 models > hide #12 models > show #12 models > ui tool show ""Show Sequence Viewer"" > sequence chain #12/A Alignment identifier is 12/A > select #12/A:65 11 atoms, 10 bonds, 1 residue, 1 model selected > select #12/A:65 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #6 models > show #6 models > hide #12 models > select #12/A:65 11 atoms, 10 bonds, 1 residue, 1 model selected > select #12/A:65 11 atoms, 10 bonds, 1 residue, 1 model selected > select #12/A:66-67 13 atoms, 12 bonds, 2 residues, 1 model selected > select #12/A:66-68 21 atoms, 20 bonds, 3 residues, 1 model selected > select #12/A:66 4 atoms, 3 bonds, 1 residue, 1 model selected > select #12/A:66 4 atoms, 3 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > select #8/A:39-40 19 atoms, 18 bonds, 2 residues, 1 model selected > select #8/A:39-119 627 atoms, 637 bonds, 81 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > select clear > select #6/A:10-37 226 atoms, 227 bonds, 28 residues, 1 model selected > select #6/A:10-111 805 atoms, 817 bonds, 102 residues, 1 model selected > select clear > select #6/A:10-85 597 atoms, 603 bonds, 76 residues, 1 model selected > select #6/A:53 12 atoms, 12 bonds, 1 residue, 1 model selected > select #6/A:53-129 599 atoms, 611 bonds, 77 residues, 1 model selected > select clear > select > #6/A:14-34,37-52,58-96,100-135,141-161,176-178,204-214,220-235,241-256,261-305,317-329,363-366,379-380,390-400,406-422,424-441,447-466,478-488,494-510,512-515,519-530,535-548,554-570,572-589,592-603,609-625,627-638,642-652,656-665,669-679,686-698,702-710,718-730,735-751,754-761,781-783,785-812 4596 atoms, 4643 bonds, 4 pseudobonds, 566 residues, 2 models selected > select clear > select #6/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:56 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel magenta > select #6/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:61 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel magenta > select #6/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #6/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel magenta > select clear > show #12 models > hide #13 models > show #13 models Drag select of 8 atoms, 10 residues, 7 bonds Drag select of 5 atoms, 5 bonds, 25 residues > show sel atoms > select clear Drag select of 24 atoms, 8 residues, 23 bonds > ui tool show Contacts > contacts sel resSeparation 3 942 contacts > select clear Drag select of 1 residues > hide #8 models > show #8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > select clear Drag select of 1 residues > select clear > hide #6 models > show #6 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #9 models > show #9 models > hide #6 models > show #6 models > hide #12 models > show #12 models > show #!11 models > hide #!11 models > hide #12 models > show #12 models > ui tool show ""Show Sequence Viewer"" > sequence chain #12/A Alignment identifier is 12/A Drag select of 1 residues > select #12/A:596 12 atoms, 12 bonds, 1 residue, 1 model selected > select #12/A:596 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear Drag select of 1 atoms, 1 residues > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > open 6KYB Summary of feedback from opening 6KYB fetched from pdb --- note | Fetching compressed mmCIF 6kyb from http://files.rcsb.org/download/6kyb.cif 6kyb title: Crystal structure of Atg18 from Saccharomyces cerevisiae [more info...] Chain information for 6kyb #14 --- Chain | Description | UniProt A B C D | Autophagy-related protein 18 | ATG18_YEAST 6kyb mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly Drag select of 82 residues > view matrix models #14,1,0,0,94.325,0,1,0,158.86,0,0,1,464.73 > select clear Drag select of 78 residues, 1 pseudobonds > ui mousemode right ""translate selected models"" > view matrix models #14,1,0,0,120.02,0,1,0,16.761,0,0,1,170.21 > view matrix models #14,1,0,0,122.69,0,1,0,18.229,0,0,1,185.13 > view matrix models #14,1,0,0,185.92,0,1,0,14.143,0,0,1,429.82 > view matrix models #14,1,0,0,192.89,0,1,0,-0.74462,0,0,1,416.31 > view matrix models #14,1,0,0,76.075,0,1,0,188.16,0,0,1,392.49 > ui mousemode right ""move picked models"" > view matrix models #14,1,0,0,120.72,0,1,0,35.94,0,0,1,193.64 > ui mousemode right select Drag select of 6 residues > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models #14,1,0,0,131.5,0,1,0,51.827,0,0,1,223.7 > ui tool show ""Show Sequence Viewer"" > sequence chain #14/A Alignment identifier is 14/A > select #14/A:32-33 14 atoms, 13 bonds, 2 residues, 1 model selected > select #14/A:32-147 908 atoms, 925 bonds, 116 residues, 1 model selected > select #14/A:87 6 atoms, 5 bonds, 1 residue, 1 model selected > select #14/A:87 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel magenta > show sel atoms > select #14/A:73 11 atoms, 10 bonds, 1 residue, 1 model selected > select #14/A:73-74 22 atoms, 21 bonds, 2 residues, 1 model selected > select clear > show #!11 models > hide #2 models > show #2 models > hide #!1 models > show #!1 models > show #3.1 models > hide #3.1 models > show #3.1 models > hide #3.1 models > show #3.1 models > hide #3.1 models > show #!4 models > hide #!4 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models Drag select of 28 residues, 11 job866_VF_postprocess_5.06A (1).mrc gaussian Drag select of 37 residues > show sel atoms > hide sel atoms > select clear > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > select #10 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #10,1,0,0,6.2398,0,1,0,-5.6027,0,0,1,16.337 > view matrix models #10,1,0,0,3.6159,0,1,0,9.7928,0,0,1,27.083 > view matrix models #10,1,0,0,2.579,0,1,0,19.963,0,0,1,36.849 > view matrix models #10,1,0,0,-15.084,0,1,0,45.434,0,0,1,3.5876 > volume #10 level 0.01271 > view matrix models #10,1,0,0,5.233,0,1,0,-3.3733,0,0,1,15.492 > show #5 models > hide #5 models > show #5 models > hide #5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > volume #11 level 0.004883 > volume #11 level 0.002362 > show #!1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #9/A Alignment identifier is 9/A > select #9/A:2250 7 atoms, 6 bonds, 1 residue, 1 model selected > select #9/A:2250 7 atoms, 6 bonds, 1 residue, 1 model selected > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show sel atoms > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select > #9/A:672-679,704-710,790-805,812-826,829-831,841-845,856-858,904-924,938-945,957-967,969-970,975-979,1012-1014,1025-1054,1061-1073,1081-1088,1100-1125,1131-1136,1142-1144,1150-1181,1189-1191,1228-1238,1251-1253,1277-1279,1296-1298,1301-1306,1310-1319,1322-1324,1328-1330,1364-1366,1369-1370,1373-1402,1412-1446,1453-1480,1484-1498,1648-1681,1684-1687,1700-1704,1706-1708,1752-1754,1823-1835,1839-1845,1861-1862,1869-1877,1879-1899,1970-1985,2011-2020,2024-2031,2063-2085,2093-2094,2156-2165,2172-2191,2223-2233,2251-2265,2270 5006 atoms, 5055 bonds, 600 residues, 1 model selected > select #9/A:2257 11 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:2257 11 atoms, 10 bonds, 1 residue, 1 model selected > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #11 level 0.001216 An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1285, description = b'out of memory', baseOperation = glBufferData, pyArgs = ( 34963, 133719744, array([[ 0, 2, 5], [ 0, 4, 2], [ 3, 0, 5], ....., GL_STATIC_DRAW, ), cArgs = ( 34963, 133719744, array([[ 0, 2, 5], [ 0, 4, 2], [ 3, 0, 5], ....., GL_STATIC_DRAW, ), cArguments = ( 34963, 133719744, array([[ 0, 2, 5], [ 0, 4, 2], [ 3, 0, 5], ....., GL_STATIC_DRAW, ) ) Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\core\updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\view.py"", line 165, in draw self._draw_scene(camera, drawings) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\view.py"", line 235, in _draw_scene draw_opaque(r, opaque_drawings) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1499, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1512, in _draw_multiple d.draw(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 752, in draw self.draw_self(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 759, in draw_self self._draw_geometry(renderer, opaque_only = any_transp) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 786, in _draw_geometry ds.activate_bindings(renderer) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1859, in activate_bindings self.update_buffers() File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1847, in update_buffers b.update_buffer_data(data) File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 2674, in update_buffer_data GL.glBufferData(btype, size, d, GL.GL_STATIC_DRAW) File ""src/latebind.pyx"", line 51, in OpenGL_accelerate.latebind.Curry.__call__ File ""C:\Program Files\ChimeraX 1.3\bin\lib\site- packages\OpenGL\GL\VERSION\GL_1_5.py"", line 89, in glBufferData return baseOperation( target, size, data, usage ) File ""src/latebind.pyx"", line 39, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src/wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glBufferData, pyArgs = ( 34963, 133719744, array([[ 0, 2, 5], [ 0, 4, 2], [ 3, 0, 5], ....., GL_STATIC_DRAW, ), cArgs = ( 34963, 133719744, array([[ 0, 2, 5], [ 0, 4, 2], [ 3, 0, 5], ....., GL_STATIC_DRAW, ), cArguments = ( 34963, 133719744, array([[ 0, 2, 5], [ 0, 4, 2], [ 3, 0, 5], ....., GL_STATIC_DRAW, ) ) > volume #11 level -0.0009031 > volume #11 level -0.001533 > volume #11 level 0.002534 > volume #11 level -0.002851 > volume #11 level -0.001361 > volume #11 level 0.004654 > volume #11 level 0.002419 > volume #11 level 0.0109 > show #!4 models > hide #!4 models > hide #!14 models > show #!14 models > hide #!11 models > show #!11 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.14756 Core Profile Forward-Compatible Context 20.40.53.01 27.20.14053.1000 OpenGL renderer: AMD Radeon(TM) Graphics OpenGL vendor: ATI Technologies Inc. Manufacturer: Microsoft Corporation Model: Surface Laptop 4 OS: Microsoft Windows 11 Home (Build 22000) Memory: 8,002,093,056 MaxProcessMemory: 137,438,953,344 CPU: 12 AMD Ryzen 5 Microsoft Surface (R) Edition OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 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: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 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: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 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 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 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: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Core can't reproduce Eric Pettersen all ChimeraX