id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5941 Crash checking if clip planes changed after 'select' command chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 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. Windows fatal exception: code 0x8001010e Thread 0x00001354 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1122 in _browse_parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1194 in parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2447 in _parse_arg File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2588 in _process_positional_arguments File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2812 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py"", line 36 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py"", line 528 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2515 in _show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2383 in show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2264 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001354 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1122 in _browse_parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1194 in parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2447 in _parse_arg File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2588 in _process_positional_arguments File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2812 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py"", line 36 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py"", line 528 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2515 in _show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2383 in show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2264 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001354 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1122 in _browse_parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1194 in parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2447 in _parse_arg File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2588 in _process_positional_arguments File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2812 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py"", line 36 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py"", line 528 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2515 in _show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2383 in show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2264 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001354 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1122 in _browse_parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1194 in parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2447 in _parse_arg File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2588 in _process_positional_arguments File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2812 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py"", line 36 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py"", line 528 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2515 in _show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2383 in show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2264 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001354 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1122 in _browse_parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1194 in parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2447 in _parse_arg File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2588 in _process_positional_arguments File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2812 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py"", line 36 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py"", line 528 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2515 in _show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2383 in show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2264 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001354 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1122 in _browse_parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 1194 in parse File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2447 in _parse_arg File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2588 in _process_positional_arguments File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py"", line 2812 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py"", line 36 in run File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py"", line 528 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2515 in _show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2383 in show_context_menu File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 2264 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main Windows fatal exception: code 0x8001010e Thread 0x00001354 (most recent call first): File ""C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\clipping.py"", line 42 in Windows fatal exception: access violation Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e Windows fatal exception: code 0x8001010e ===== Log before crash start ===== > ui windowfill toggle > open D:\RawData\BDC\processed_models\PCC_mutation_mapped_v0.1.cxs format > session opened ChimeraX session > close > open D:\RawData\BDC\models\PYC-coot-8.pdb format pdb Summary of feedback from opening D:\RawData\BDC\models\PYC-coot-8.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 22 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 23 BOND : 0.006 0.063 21524 Ignored bad PDB record found on line 24 ANGLE : 0.886 10.505 29172 18 messages similar to the above omitted Chain information for PYC-coot-8.pdb #1 --- Chain | Description A B C D | No description available > show target m > interfaces ~solvent 6 buried areas: A B 2132, C D 2128, B D 1323, A C 1322, B C 348, A D 348 > hide cartoons > show cartoons > hide atoms > color bypolymer > color bychain > select ::name=""LIG"" 60 atoms, 64 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > show sel cartoons > hide sel cartoons > show sel cartoons > select ::name=""LIG"" 60 atoms, 64 bonds, 4 residues, 1 model selected > show sel atoms > select clear > hide sel atoms > select clear > select ::34 Expected an objects specifier or a keyword > select :34 Nothing selected > open 6ybp Summary of feedback from opening 6ybp fetched from pdb --- notes | Fetching compressed mmCIF 6ybp from http://files.rcsb.org/download/6ybp.cif Fetching CCD BTI from http://ligand-expo.rcsb.org/reports/B/BTI/BTI.cif 6ybp title: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA [more info...] Chain information for 6ybp #2 --- Chain | Description | UniProt A B C D E F | Propionyl-CoA carboxylase β chain | C5AP75_METEA G H I J K L | Propionyl-CoA carboxylase α subunit | C5AWU5_METEA Non-standard residues in 6ybp #2 --- BTI — 5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal COA — coenzyme A > undo > close #2 > open 2qf7 2qf7 title: Crystal structure of a complete multifunctional pyruvate carboxylase from Rhizobium etli [more info...] Chain information for 2qf7 #2 --- Chain | Description | UniProt A B | Pyruvate carboxylase protein | Q2K340_RHIEC Non-standard residues in 2qf7 #2 --- AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate); adenosine-5'-diphosphate monothiophosphate) CL — chloride ion COA — coenzyme A FMT — formic acid GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion ZN — zinc ion 2qf7 mmCIF Assemblies --- 1| author_and_software_defined_assembly > interfaces ~solvent 7 buried areas: #2/A #2/B 2265, #1/A #1/B 2132, #1/C #1/D 2128, #1/B #1/D 1323, #1/A #1/C 1322, #1/B #1/C 348, #1/A #1/D 348 > undo > select clear > show sel cartoons > select clear > hide sel cartoons > hide sel atoms > hide sel surfaces > select ::name=""HOH"" 1318 atoms, 1318 residues, 1 model selected > hide sel atoms > hide sel cartoons > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-0.53715,0,1,0,3.2851,0,0,1,16.211 > view matrix models #1,1,0,0,7.3056,0,1,0,4.4588,0,0,1,20.393 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.41627,0.16295,0.89452,74.815,0.071441,-0.97491,0.21084,242.09,0.90643,0.15167,0.39418,-54.184 > view matrix models > #1,-0.55986,-0.10197,0.82229,139.65,0.70393,0.46497,0.53693,-82.044,-0.43709,0.87943,-0.18854,99.328 > view matrix models > #1,-0.87372,-0.32961,0.35774,269,-0.14405,0.87776,0.45693,-12.617,-0.46462,0.3477,-0.81439,250.12 > select #2 17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected > view matrix models > #2,-0.52914,0.26396,-0.80644,198.85,-0.31461,-0.94368,-0.10245,246.5,-0.78806,0.1995,0.58238,95.949 > view matrix models > #2,-0.2746,-0.57438,-0.77116,249.47,0.60023,-0.72894,0.3292,89.808,-0.75122,-0.37247,0.54492,150.55 > ~select #2 Nothing selected > ui mousemode right ""translate selected models"" > select #1 21044 atoms, 21524 bonds, 2736 residues, 1 model selected > view matrix models > #1,-0.87372,-0.32961,0.35774,265.06,-0.14405,0.87776,0.45693,-27.335,-0.46462,0.3477,-0.81439,238.12 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.83135,-0.36119,0.42238,255.96,0.040194,0.71894,0.69391,-58.74,-0.5543,0.59386,-0.58317,189.32 > view matrix models > #1,-0.66165,-0.60148,0.44771,262.71,0.70068,-0.28338,0.65479,-7.0059,-0.26697,0.74694,0.60894,-11.748 > view matrix models > #1,-0.63836,-0.71318,0.28962,293.51,0.73772,-0.67424,-0.034258,122.9,0.2197,0.19179,0.95653,-43.23 > view matrix models > #1,-0.69872,-0.53067,0.47977,254.28,0.56886,-0.0054734,0.82241,-46.882,-0.4338,0.84756,0.3057,33.082 > view matrix models > #1,-0.19867,-0.93593,0.29079,263.46,-0.65247,0.3477,0.67333,90.38,-0.73131,-0.055962,-0.67975,314.7 > view matrix models > #1,-0.10678,-0.92809,0.35672,241.94,-0.24843,0.3723,0.89425,5.2681,-0.96275,0.0068645,-0.27032,289.75 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.10678,-0.92809,0.35672,235.48,-0.24843,0.3723,0.89425,-9.9339,-0.96275,0.0068645,-0.27032,195.86 > hide sel cartoons > view matrix models > #1,-0.10678,-0.92809,0.35672,263.26,-0.24843,0.3723,0.89425,-1.3379,-0.96275,0.0068645,-0.27032,185.74 > view matrix models > #1,-0.10678,-0.92809,0.35672,260.14,-0.24843,0.3723,0.89425,-10.37,-0.96275,0.0068645,-0.27032,191.11 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.14264,-0.79326,0.59194,172.89,-0.28195,0.54072,0.79255,-18.63,-0.94877,-0.27995,-0.14654,217.65 > view matrix models > #1,0.11385,-0.71688,0.68784,154.65,-0.28635,0.63928,0.71367,-23.516,-0.95134,-0.27821,-0.13249,216.14 > view matrix models > #1,0.39486,-0.57205,0.71892,84.427,-0.12476,0.74187,0.65884,-57.708,-0.91023,-0.34984,0.22156,178.78 > view matrix models > #1,-0.11202,-0.99331,0.028108,308.74,0.12433,0.014054,0.99214,-26.279,-0.9859,0.11464,0.12192,132.38 > view matrix models > #1,-0.11296,-0.99204,0.055637,305.45,0.12846,0.040944,0.99087,-30.847,-0.98526,0.11908,0.12281,131.51 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.11296,-0.99204,0.055637,301.14,0.12846,0.040944,0.99087,-47.442,-0.98526,0.11908,0.12281,130.8 > view matrix models > #1,-0.11296,-0.99204,0.055637,317.72,0.12846,0.040944,0.99087,-56.543,-0.98526,0.11908,0.12281,130.83 > view matrix models > #1,-0.11296,-0.99204,0.055637,321.2,0.12846,0.040944,0.99087,-50.817,-0.98526,0.11908,0.12281,131.13 > view matrix models > #1,-0.11296,-0.99204,0.055637,321.33,0.12846,0.040944,0.99087,-50.909,-0.98526,0.11908,0.12281,131.42 > view matrix models > #1,-0.11296,-0.99204,0.055637,320.07,0.12846,0.040944,0.99087,-52.927,-0.98526,0.11908,0.12281,130.88 > show sel cartoons > select clear > hide sel cartoons Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > view matrix models > #2,-0.2746,-0.57438,-0.77116,248.67,0.60023,-0.72894,0.3292,89.916,-0.75122,-0.37247,0.54492,150.03 > view matrix models > #2,-0.2746,-0.57438,-0.77116,248.85,0.60023,-0.72894,0.3292,90.309,-0.75122,-0.37247,0.54492,150.02 > view matrix models > #2,-0.2746,-0.57438,-0.77116,247.13,0.60023,-0.72894,0.3292,87.773,-0.75122,-0.37247,0.54492,149.89 > view matrix models > #2,-0.2746,-0.57438,-0.77116,248.29,0.60023,-0.72894,0.3292,90.351,-0.75122,-0.37247,0.54492,150.08 > view matrix models > #2,-0.2746,-0.57438,-0.77116,248.45,0.60023,-0.72894,0.3292,89.3,-0.75122,-0.37247,0.54492,150.1 > view matrix models > #2,-0.2746,-0.57438,-0.77116,247.54,0.60023,-0.72894,0.3292,89.416,-0.75122,-0.37247,0.54492,150.02 > view matrix models > #2,-0.2746,-0.57438,-0.77116,248.01,0.60023,-0.72894,0.3292,88.51,-0.75122,-0.37247,0.54492,150.01 > view matrix models > #2,-0.2746,-0.57438,-0.77116,247.04,0.60023,-0.72894,0.3292,89.013,-0.75122,-0.37247,0.54492,151.21 > ui tool show Matchmaker > matchmaker #!2 to #1 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 PYC-coot-8.pdb, chain A (#1) with 2qf7, chain A (#2), sequence alignment score = 1834.1 RMSD between 411 pruned atom pairs is 1.055 angstroms; (across all 673 pairs: 15.575) > show sel cartoons > select clear > hide sel cartoons > hide sel atoms > hide sel cartoons > hide sel atoms > select #1/A:1144 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select ::name=""LIG"" 60 atoms, 64 bonds, 4 residues, 1 model selected > select ::name=""AGS"" 62 atoms, 66 bonds, 2 residues, 1 model selected > hide sel atoms > select clear > show sel cartoons > hide sel cartoons > open 4qsl Summary of feedback from opening 4qsl fetched from pdb --- note | Fetching compressed mmCIF 4qsl from http://files.rcsb.org/download/4qsl.cif 4qsl title: Crystal Structure of Listeria Monocytogenes Pyruvate Carboxylase [more info...] Chain information for 4qsl #3 --- Chain | Description | UniProt A B C D E F G H | Pyruvate carboxylase | W6G6F5_LISMN 4qsl mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #3/A#3/B#3/C#3/D#3/E#3/F#3/G#3/H 60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected > select #3/B:223@OD1 1 atom, 1 residue, 1 model selected > select #3/A#3/B#3/C#3/D#3/E#3/F#3/G#3/H 60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected > select subtract #3/B:270@OD1 60494 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected > select subtract #3/B:2@ND2 60493 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected > select subtract #3/B:951@CG2 60492 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected Drag select of 157 atoms > select clear > select #3/A 7969 atoms, 8136 bonds, 1 pseudobond, 1052 residues, 2 models selected > select #3/B 7492 atoms, 7639 bonds, 4 pseudobonds, 1031 residues, 2 models selected > select #3/A,C,D,E,F,G 45122 atoms, 46023 bonds, 13 pseudobonds, 6047 residues, 2 models selected > hide sel atoms > hide sel cartoons > select #3/A,C,D,E,F,G,H 53003 atoms, 54065 bonds, 14 pseudobonds, 7076 residues, 2 models selected > hide sel cartoons > hide sel atoms > hide sel cartoons > hide sel atoms > select #3/B 7492 atoms, 7639 bonds, 4 pseudobonds, 1031 residues, 2 models selected > hide sel atoms > show sel cartoons > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,267.48,0,1,0,56.193,0,0,1,-17.252 > view matrix models #3,1,0,0,250.82,0,1,0,53.244,0,0,1,-14.201 > select clear > select #3/B 7492 atoms, 7639 bonds, 4 pseudobonds, 1031 residues, 2 models selected > view matrix models #3,1,0,0,215.16,0,1,0,-12.612,0,0,1,-57.398 > view matrix models #3,1,0,0,279.56,0,1,0,113.22,0,0,1,9.4109 > view matrix models #3,1,0,0,278.78,0,1,0,112.15,0,0,1,7.8829 > ui tool show Matchmaker > matchmaker #!2-3 to #1 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 PYC-coot-8.pdb, chain A (#1) with 2qf7, chain A (#2), sequence alignment score = 1834.1 RMSD between 411 pruned atom pairs is 1.055 angstroms; (across all 673 pairs: 15.575) Matchmaker PYC-coot-8.pdb, chain A (#1) with 4qsl, chain A (#3), sequence alignment score = 1879.2 RMSD between 467 pruned atom pairs is 0.893 angstroms; (across all 596 pairs: 2.247) > select #3/A#3/B#3/C#3/D#3/E#3/F#3/G#3/H 60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected > show sel cartoons > select #3/B,C,D,E,F,G,H 52526 atoms, 53568 bonds, 17 pseudobonds, 7055 residues, 2 models selected > hide sel cartoons > select #2/A 8858 atoms, 8332 bonds, 24 pseudobonds, 1772 residues, 3 models selected > select #3/A 7969 atoms, 8136 bonds, 1 pseudobond, 1052 residues, 2 models selected > color (#!3 & sel) magenta > select clear > select #3/A 7969 atoms, 8136 bonds, 1 pseudobond, 1052 residues, 2 models selected > color (#!3 & sel) hot pink > select #2/A:448 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #3/A:1140 Nothing selected > open 3bg5 Summary of feedback from opening 3bg5 fetched from pdb --- notes | Fetching compressed mmCIF 3bg5 from http://files.rcsb.org/download/3bg5.cif Fetching CCD MN from http://ligand-expo.rcsb.org/reports/M/MN/MN.cif Fetching CCD PYR from http://ligand-expo.rcsb.org/reports/P/PYR/PYR.cif Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif 3bg5 title: Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase [more info...] Chain information for 3bg5 #4 --- Chain | Description | UniProt A B C D | Pyruvate carboxylase | Q99UY8_STAAM Non-standard residues in 3bg5 #4 --- ATP — adenosine-5'-triphosphate BTI — 5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal MN — manganese (II) ion PYR — pyruvic acid 3bg5 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly 3| software_defined_assembly > ui tool show Matchmaker > matchmaker #!2-4 to #1 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 PYC-coot-8.pdb, chain A (#1) with 2qf7, chain A (#2), sequence alignment score = 1834.1 RMSD between 411 pruned atom pairs is 1.055 angstroms; (across all 673 pairs: 15.575) Matchmaker PYC-coot-8.pdb, chain A (#1) with 4qsl, chain A (#3), sequence alignment score = 1879.2 RMSD between 467 pruned atom pairs is 0.893 angstroms; (across all 596 pairs: 2.247) Matchmaker PYC-coot-8.pdb, chain A (#1) with 3bg5, chain D (#4), sequence alignment score = 1919.7 RMSD between 438 pruned atom pairs is 0.986 angstroms; (across all 669 pairs: 4.966) > select #4/D 8435 atoms, 8593 bonds, 3 pseudobonds, 1070 residues, 3 models selected > select #4/A,B,C 26003 atoms, 26499 bonds, 4 pseudobonds, 3289 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #2 17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected > color (#!2 & sel) white > select #3 60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected > color (#!3 & sel) light gray > color (#!3 & sel) gray > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > color (#!4 & sel) dim gray > select clear > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > color (#!4 & sel) black > select clear > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > ui tool show ""Color Actions"" > color sel light slate gray > select #1 21044 atoms, 21524 bonds, 2736 residues, 1 model selected > color sel hot pink > select clear > select #3 60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected > color (#!3 & sel) dim gray > select clear > close #3 > select #2 17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > color (#!4 & sel) gray > select clear > select #2 17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected > color (#!2 & sel) cornflower blue > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > color (#!4 & sel) light sea green > select clear > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > color (#!4 & sel) cyan > select clear > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > color (#!4 & sel) light gray > select clear > select #43. Expected an objects specifier or a keyword > select #4 34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected > hide sel atoms > select ::name=""BTI"" 60 atoms, 64 bonds, 4 residues, 1 model selected > show sel atoms > select #4/A,B,C 26003 atoms, 26499 bonds, 4 pseudobonds, 3289 residues, 3 models selected > hide sel atoms > select #1,2,4 72700 atoms, 72827 bonds, 59 pseudobonds, 10524 residues, 7 models selected > color sel byhetero > select clear > select ::name=""LIG"" 60 atoms, 64 bonds, 4 residues, 1 model selected > select clear > save D:/RawData/BDC/processed_models/PYC-2qf7-3bg5-align.tif width 1509 > height 859 supersample 3 transparentBackground true > hide #!2 models > hide #2.2 models > hide #!4 models > hide #2.1 models > select #1 21044 atoms, 21524 bonds, 2736 residues, 1 model selected > show sel cartoons > color sel bychain > select #1/A 5261 atoms, 5381 bonds, 684 residues, 1 model selected > select #1/B 5261 atoms, 5381 bonds, 684 residues, 1 model selected > color sel hot pink > select clear > select ::name=""LIG"" 60 atoms, 64 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select #1:1144 36 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > select clear > save D:/RawData/BDC/processed_models/PYC-overall.tif width 1509 height 859 > supersample 3 transparentBackground true > select clear > select ::name=""LIG"" 60 atoms, 64 bonds, 4 residues, 1 model selected > show sel atoms > select #1:1144 36 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > hide sel cartoons > hide sel atoms > hide sel cartoons > hide sel atoms > show sel cartoons > color sel byhetero > select clear > select #1/B:name=""LIG"" Expected an objects specifier or a keyword > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > color sel dim gray > select clear > select #1/B 5261 atoms, 5381 bonds, 684 residues, 1 model selected > color sel hot pink > color sel byhetero > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > color sel dim gray > select clear > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641 NE 3 hydrogen bonds found > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641 NE 3 hydrogen bonds found > ui tool show H-Bonds > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641 NE 3 hydrogen bonds found > select clear > ui tool show ""Side View"" > select clear > ui tool show Contacts > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > contacts sel resSeparation 5 72 contacts > contacts sel resSeparation 5 showDist true 72 contacts > contacts sel showDist true 72 contacts > hide sel atoms > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641 NE 2514 hydrogen bonds found > ~hbonds > select clear > hide sel atoms > hide sel cartoons > hide sel atoms > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641 NE 3 hydrogen bonds found > contacts sel showDist true 72 contacts > contacts sel intraModel false showDist true 49 contacts > select #1/A:877 9 atoms, 8 bonds, 1 residue, 1 model selected > select subtract #1/A:942 1205 atoms, 151 residues, 1 model selected > select subtract #1/A:916 1197 atoms, 150 residues, 1 model selected > select subtract #1/A:941 1190 atoms, 149 residues, 1 model selected > select subtract #1/B:1147 1183 atoms, 148 residues, 1 model selected > select subtract #1/B:1146 1174 atoms, 147 residues, 1 model selected > select subtract #1/B:1145 1166 atoms, 146 residues, 1 model selected > select subtract #1/B:1144 1157 atoms, 145 residues, 1 model selected > select subtract #1/B:1143 1149 atoms, 144 residues, 1 model selected > select subtract #1/B:1142 1144 atoms, 143 residues, 1 model selected > select subtract #1/A:881 1136 atoms, 142 residues, 1 model selected > select subtract #1/A:880 1130 atoms, 141 residues, 1 model selected > select subtract #1/A:920 1119 atoms, 140 residues, 1 model selected > select subtract #1/B:1148 1112 atoms, 139 residues, 1 model selected > select subtract #1/B:1116 1104 atoms, 138 residues, 1 model selected > select subtract #1/B:1115 1097 atoms, 137 residues, 1 model selected > select subtract #1/B:1117 1090 atoms, 136 residues, 1 model selected > select subtract #1/A:924 1082 atoms, 135 residues, 1 model selected > select subtract #1/A:923 1073 atoms, 134 residues, 1 model selected > select subtract #1/A:939 1067 atoms, 133 residues, 1 model selected > select subtract #1/A:938 1059 atoms, 132 residues, 1 model selected > select subtract #1/A:937 1050 atoms, 131 residues, 1 model selected > select subtract #1/A:936 1041 atoms, 130 residues, 1 model selected > select subtract #1/A:969 1032 atoms, 129 residues, 1 model selected > select subtract #1/B:1134 1028 atoms, 128 residues, 1 model selected > select add #1/B:1135 1037 atoms, 8 bonds, 129 residues, 1 model selected > select subtract #1/B:1150 1030 atoms, 8 bonds, 128 residues, 1 model selected > select subtract #1/B:1135 1021 atoms, 127 residues, 1 model selected > select subtract #1/B:1133 1012 atoms, 126 residues, 1 model selected > select subtract #1/B:1152 1005 atoms, 125 residues, 1 model selected > select subtract #1/B:1171 997 atoms, 124 residues, 1 model selected > select subtract #1/A:617 986 atoms, 123 residues, 1 model selected > select subtract #1/B:1106 977 atoms, 122 residues, 1 model selected > select subtract #1/B:1063 969 atoms, 121 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select #1/B:1146 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > contacts sel intraModel false showDist true 49 contacts > contacts sel showDist true 72 contacts > select #1/A:877 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:651 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > contacts makePseudobonds false 445143 contacts > contacts makePseudobonds false 445143 contacts > select #1/A:876 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > save D:/RawData/BDC/processed_models/PYC-biotin-pocket.tif width 1508 height > 859 supersample 3 transparentBackground true > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C #1/D Alignment identifier is 1 QWindowsWindow::setGeometry: Unable to set geometry 3840x2583+0+57 (frame: 3872x2671-16-15) on QWidgetWindow/""MainWindowClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 3840x2268+0+56 (frame: 3872x2356-16-16) margins: 16, 72, 16, 16 minimum size: 477x861 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1463,2671 maxtrack=0,0) > select > #1/A-D:496-510,541-558,572-577,584-597,611-617,623-633,656-669,683-695,720-732,749-762,779-789,799-801,810-816,828-844,846-848,850-852,859-864,868-880,887-900,910-924,929-932,934-936,942-949,963-967,987-998,1004-1012,1014-1026,1030-1032,1035-1040 8884 atoms, 8948 bonds, 1120 residues, 1 model selected > select clear > select #1/B::name=""LIG"" 15 atoms, 16 bonds, 1 residue, 1 model selected > contacts makePseudobonds false 445143 contacts > contacts 445143 contacts > contacts sel showDist true 72 contacts > select clear > hide sel cartoons > show sel cartoons > hide sel atoms > select #1::name=""LIG"" 60 atoms, 64 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select #1:1144 36 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select #1/A:870 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > ui tool show Distances No distances to delete! > ui tool show Contacts > contacts makePseudobonds false 445143 contacts QWindowsWindow::setGeometry: Unable to set geometry 1398x304+6788+1726 (frame: 1420x360+6777+1681) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x304+6788+1726 (frame: 1423x360+6777+1681) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1380x300+6786+1722 (frame: 1402x356+6775+1677) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x300+6786+1722 (frame: 1423x356+6775+1677) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1350x292+6784+1718 (frame: 1372x348+6773+1673) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x292+6784+1718 (frame: 1423x348+6773+1673) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1310x280+6780+1710 (frame: 1332x336+6769+1665) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x280+6780+1710 (frame: 1423x336+6769+1665) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1256x266+6776+1700 (frame: 1278x322+6765+1655) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6776+1700 (frame: 1423x326+6765+1655) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1190x250+6770+1688 (frame: 1212x306+6759+1643) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6770+1688 (frame: 1423x326+6759+1643) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1120x228+6762+1676 (frame: 1142x284+6751+1631) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6762+1676 (frame: 1423x326+6751+1631) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1060x214+6756+1664 (frame: 1082x270+6745+1619) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6756+1664 (frame: 1423x326+6745+1619) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 1010x202+6752+1654 (frame: 1032x258+6741+1609) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6752+1654 (frame: 1423x326+6741+1609) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 974x190+6748+1648 (frame: 996x246+6737+1603) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6748+1648 (frame: 1423x326+6737+1603) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 950x184+6746+1644 (frame: 972x240+6735+1599) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6746+1644 (frame: 1423x326+6735+1599) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 936x180+6746+1642 (frame: 958x236+6735+1597) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6746+1642 (frame: 1423x326+6735+1597) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) QWindowsWindow::setGeometry: Unable to set geometry 934x180+6746+1642 (frame: 956x236+6735+1597) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 1401x270+6746+1642 (frame: 1423x326+6735+1597) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326 maxtrack=1572883,1572917) > select clear > show sel atoms > color sel byhetero > select clear Restriction atom specifier must not be blank > contacts sel restrict both makePseudobonds false 452 contacts > select clear > select #1:495-523 876 atoms, 900 bonds, 116 residues, 1 model selected > select #1:495-523,1032-1092 2832 atoms, 2876 bonds, 360 residues, 1 model selected > select ~sel 69868 atoms, 69951 bonds, 63 pseudobonds, 10164 residues, 9 models selected > hide sel & #1 cartoons > hide sel & #1 atoms > select #1/A,B:495-523,1032-1092 1416 atoms, 1438 bonds, 180 residues, 1 model selected > select #1/D,B:495-523,1032-1092 1416 atoms, 1438 bonds, 180 residues, 1 model selected > select #1/D,C:495-523,1032-1092 1416 atoms, 1438 bonds, 180 residues, 1 model selected > select #1/D,A:495-523,1032-1092 1416 atoms, 1438 bonds, 180 residues, 1 model selected > hide sel cartoons > save D:/RawData/BDC/processed_models/PYC-BT-top.tif width 1449 height 859 > supersample 3 transparentBackground true > save D:/RawData/BDC/processed_models/PYC-BT-side.tif width 1449 height 859 > supersample 3 transparentBackground true > select #1/B 5261 atoms, 5381 bonds, 684 residues, 1 model selected > select #1/C' Nothing selected > select #1/C 5261 atoms, 5381 bonds, 684 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #1/B 5261 atoms, 5381 bonds, 684 residues, 1 model selected > hide sel atoms > select clear > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Fayang\Desktop\movie1.mp4 Movie saved to \C:Users\\...\Desktop\movie1.mp4 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Fayang\Desktop\movie2.mp4 Movie saved to \C:Users\\...\Desktop\movie2.mp4 > undo > select clear > select #1/B 5261 atoms, 5381 bonds, 684 residues, 1 model selected > select #1/C 5261 atoms, 5381 bonds, 684 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #1/B:1063 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:1064 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #1/B:1063 13 atoms, 11 bonds, 2 residues, 1 model selected > select add #1/B:1066 19 atoms, 16 bonds, 3 residues, 1 model selected > select add #1/B:1075 28 atoms, 24 bonds, 4 residues, 1 model selected > select add #1/B:1077 39 atoms, 35 bonds, 5 residues, 1 model selected > select add #1/B:1084 47 atoms, 42 bonds, 6 residues, 1 model selected > select add #1/B:1065 54 atoms, 48 bonds, 7 residues, 1 model selected > show sel atoms > select #1/B:1065 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/B:1063 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1/B:1064 13 atoms, 11 bonds, 2 residues, 1 model selected > select add #1/B:1066 19 atoms, 16 bonds, 3 residues, 1 model selected > select add #1/B:1075 28 atoms, 24 bonds, 4 residues, 1 model selected > select add #1/B:1077 39 atoms, 35 bonds, 5 residues, 1 model selected > select add #1/B:1084 47 atoms, 42 bonds, 6 residues, 1 model selected QWindowsWindow::setGeometry: Unable to set geometry 7102x906-3046+806 (frame: 7134x994-3062+734) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY1"". Resulting geometry: 7684x1515-3041+833 (frame: 7716x1603-3057+761) margins: 16, 72, 16, 16 minimum size: 62x37 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=218,199 maxtrack=1572893,1572949) > select #1/C 5261 atoms, 5381 bonds, 684 residues, 1 model selected > select > #1/A-D:564-567,604-608,639-644,673-677,699-706,737-742,767-772,793-796,1048-1051,1057-1065,1073-1080,1083-1090,1111-1113,1139-1141,1146-1148,1173-1176 2816 atoms, 2804 bonds, 344 residues, 1 model selected > select #1/A-D:1031-1032 56 atoms, 52 bonds, 8 residues, 1 model selected > select #1/A-D:1031-1092 1988 atoms, 2008 bonds, 248 residues, 1 model selected ===== 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 QWindowsWindow::setGeometry: Unable to set geometry 5760x934+2152+1118 (frame: 5782x990+2141+1073) on QWidgetWindow/""QDockWidgetClassWindow"" on ""\\\\.\DISPLAY2"". Resulting geometry: 3453x557+2147+1091 (frame: 3475x613+2136+1046) margins: 11, 45, 11, 11 minimum size: 600x289 maximum size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1222,634 maxtrack=1048596,1048630) OpenGL version: 3.3.0 NVIDIA 471.35 OpenGL renderer: NVIDIA GeForce RTX 2060 with Max-Q Design/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: XPS 17 9700 OS: Microsoft Windows 10 专业版 (Build 19044) Memory: 68,451,766,272 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-10885H CPU @ 2.40GHz OSLanguage: zh-CN Locale: ('zh_CN', 'cp936') 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 Graphics can't reproduce all ChimeraX