id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4934 Crash computing clashes macbas@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Last time you used ChimeraX it crashed. Fatal Python error: Aborted Thread 0x00001eec (most recent call first): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py"", line 306 in wait File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py"", line 558 in wait File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py"", line 1252 in run File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py"", line 932 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\threading.py"", line 890 in _bootstrap Current thread 0x000005c8 (most recent call first): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py"", line 293 in event_loop File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py"", line 866 in init File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py"", line 1015 in File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\runpy.py"", line 194 in _run_module_as_main Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open C:\\\Users\\\Maciek\\\Desktop\\\FinO_proteins.cxs Log from Thu Jul 22 11:19:18 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open C:\\\Users\\\Maciek\\\Desktop\\\FinO_proteins.cxs Log from Wed Jul 21 14:22:07 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open C:\\\Users\\\Maciek\\\Desktop\\\FinO_proteins.cxs Log from Tue Jul 20 15:35:07 2021UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""F:/Roboczy_folder/PyMol data/ProQ_czyste.pse"" Unrecognized file suffix '.pse' > open > C:\Users\Maciek\Desktop\Data.copy\\#Studia_doktoranckie_Zakład_Biochemii_zrzut_21.11.19\granty\Preludium\Preludium_2021\robocze_pliki\Structural_alignments\Complete_FopA_strucutre\model1.pdb > format pdb Chain information for model1.pdb #1 --- Chain | Description A | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:1 16 atoms, 15 bonds, 1 residue, 1 model selected > select /A:1-83 1362 atoms, 1378 bonds, 83 residues, 1 model selected > delete :1-83 > open > F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/ProQ.cif Summary of feedback from opening F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/ProQ.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Atom H is not in the residue template for MET /A:1 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for ProQ.cif #2 --- Chain | Description A | No description available > set bgColor white Drag select of 4 residues Drag select of 4 residues > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,12.942,0,1,0,28.822,0,0,1,53.637 > view matrix models #2,1,0,0,6.3703,0,1,0,11.783,0,0,1,23.71 > select clear > select #1/A:141 14 atoms, 13 bonds, 1 residue, 1 model selected > view matrix models #1,1,0,0,-93.527,0,1,0,-56.182,0,0,1,-31.873 Drag select of 8 residues > view matrix models #1,1,0,0,-104.36,0,1,0,-51.316,0,0,1,-29.654 > select clear > select #2/A:39 20 atoms, 20 bonds, 1 residue, 1 model selected > view matrix models #2,1,0,0,7.8377,0,1,0,19.276,0,0,1,20.375 > show surfaces > select clear > select #2/A:62@CG 1 atom, 1 residue, 1 model selected > view matrix models #2,1,0,0,30.309,0,1,0,44.846,0,0,1,0.51203 Drag select of model1.pdb_A SES surface, 470 of 149100 triangles, 3 residues Drag select of model1.pdb_A SES surface, 1204 of 149100 triangles, 4 residues > view matrix models #1,1,0,0,-84.088,0,1,0,-32.763,0,0,1,-24.099 > view matrix models #1,1,0,0,-84.038,0,1,0,-32.357,0,0,1,-23.877 > select #1/A:110@CG2 1 atom, 1 residue, 1 model selected > view matrix models #1,1,0,0,-81.56,0,1,0,-33.393,0,0,1,-25.464 > view matrix models #1,1,0,0,-82.188,0,1,0,-35.326,0,0,1,-26.368 > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.75178,0.31072,0.58162,-126.55,-0.045219,0.90424,-0.42463,3.4339,-0.65787,0.29293,0.69383,19.179 > select #2/A:36@HB 1 atom, 1 residue, 1 model selected > view matrix models > #2,0.73253,-0.45298,0.50815,29.443,0.23577,0.86909,0.43485,45.548,-0.6386,-0.19873,0.74343,-1.4536 > view matrix models > #2,0.70446,-0.44583,0.55224,29.368,0.23318,0.88028,0.41321,45.541,-0.67034,-0.16232,0.72408,-1.5369 > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" > view matrix models > #2,0.70446,-0.44583,0.55224,27.052,0.23318,0.88028,0.41321,43.636,-0.67034,-0.16232,0.72408,0.93157 > view matrix models > #1,0.75178,0.31072,0.58162,-124.32,-0.045219,0.90424,-0.42463,2.407,-0.65787,0.29293,0.69383,16.982 > select clear > save C:/Users/Maciek/Desktop/FinO_proteins.cxs > open 1dvo 1dvo title: The X-ray crystal structure of fino, A repressor of bacterial conjugation [more info...] Chain information for 1dvo #3 --- Chain | Description A | fertility inhibition protein O > show surfaces > view matrix models #3,1,0,0,-35.537,0,1,0,48.703,0,0,1,33.157 > view matrix models #3,1,0,0,-36.024,0,1,0,44.538,0,0,1,33.904 > tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > delete #3:33-72 > reneame #1 FopA Unknown command: reneame #1 FopA > rename #1 FopA > rename #3 FinO > rename #2 ProQ > ui mousemode right ""rotate selected models"" > select #1/A:193@CB 1 atom, 1 residue, 1 model selected > view matrix models > #1,0.73395,0.10374,0.67124,-112.7,-0.072924,0.99459,-0.073976,-25.703,-0.67528,0.0053447,0.73754,37.907 > select #3/A:130@CB 1 atom, 1 residue, 1 model selected > view matrix models > #3,0.51046,0.62568,-0.58988,3.4568,0.54159,-0.76676,-0.34462,67.578,-0.66792,-0.14356,-0.73026,149.69 > ui mousemode right ""move picked models"" > view matrix models > #3,0.51046,0.62568,-0.58988,-5.364,0.54159,-0.76676,-0.34462,81.751,-0.66792,-0.14356,-0.73026,144.86 > view matrix models > #3,0.51046,0.62568,-0.58988,-18.44,0.54159,-0.76676,-0.34462,63.762,-0.66792,-0.14356,-0.73026,125.94 > select #3/A:128@CG2 1 atom, 1 residue, 1 model selected > view matrix models > #3,0.51046,0.62568,-0.58988,-18.209,0.54159,-0.76676,-0.34462,64.187,-0.66792,-0.14356,-0.73026,125.51 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.61278,0.23475,-0.75458,-7.4367,0.75613,-0.45173,0.4735,9.5112,-0.22971,-0.86072,-0.45431,106.47 > ui mousemode right ""move picked models"" > view matrix models > #3,0.61278,0.23475,-0.75458,-8.2744,0.75613,-0.45173,0.4735,7.5345,-0.22971,-0.86072,-0.45431,108.32 > save C:/Users/Maciek/Desktop/FinO_proteins.cxs > open 3mw6 3mw6 title: Crystal structure of NMB1681 from Neisseria meningitidis MC58, a FinO-like RNA chaperone [more info...] Chain information for 3mw6 #4 --- Chain | Description A B C D E F | uncharacterized protein NMB1681 Non-standard residues in 3mw6 #4 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 3mw6 mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly 3| software_defined_assembly 4| software_defined_assembly > delete #4/B-F > delete solvent > style #4 cartoon Expected a keyword > style #4 cartoon atoms Expected a keyword > style #4 atoms cartoon Expected a keyword > usage style style [objects] [atomStyle] [dashes an integer] [ringFill ringFill] — change atom and bond depiction objects: an objects specifier or nothing atomStyle: one of ball, sphere, or stick or nothing ringFill: one of off, on, thick, or thin > style #4 cartoon Expected a keyword > style #4 > style #4 ball off Expected a keyword > style #4 sphere FALSE Expected a keyword > style #4 sphere False Expected a keyword > style #4 sphere false Expected a keyword > style #4 sphere off Expected a keyword > hide :4 sphere Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide :4 atoms sphere Expected ',' or a keyword > hide :4 spehe atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > style sel sphere Changed 1 atom style > select #4/A:49@N 1 atom, 1 residue, 1 model selected > select #4 959 atoms, 975 bonds, 122 residues, 1 model selected > style sel sphere Changed 959 atom styles > style sel stick Changed 959 atom styles > style sel stick Changed 959 atom styles > style sel sphere Changed 959 atom styles > style sel ball Changed 959 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 959 atom styles > style sel sphere Changed 959 atom styles > style sel ball Changed 959 atom styles > style sel sphere Changed 959 atom styles > show sel atoms > show sel atoms > show sel atoms > show sel cartoons > show sel cartoons > hide sel atoms > show sel surfaces > select #4/A:45@O 1 atom, 1 residue, 1 model selected > view matrix models #4,1,0,0,-83.513,0,1,0,6.3887,0,0,1,91.272 > view matrix models #4,1,0,0,-62.355,0,1,0,44.93,0,0,1,110.07 > view matrix models #4,1,0,0,-75.954,0,1,0,34.991,0,0,1,133.14 > view matrix models #4,1,0,0,-78.076,0,1,0,34.692,0,0,1,135.32 > view matrix models #4,1,0,0,-77.818,0,1,0,35.594,0,0,1,134.07 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.93355,-0.20658,0.29295,-70.557,0.26346,0.94959,-0.16994,34.041,-0.24307,0.23582,0.94091,129.57 > view matrix models > #4,0.99972,-0.015582,0.018014,-77.327,0.015825,0.99978,-0.013415,35.412,-0.017801,0.013696,0.99975,133.85 > view matrix models > #4,0.99964,0.017743,-0.019926,-78.37,-0.017438,0.99973,0.015361,35.81,0.020193,-0.015008,0.99968,134.3 > view matrix models > #4,0.96546,0.18607,-0.18237,-83.237,-0.15651,0.9738,0.16498,38.275,0.20829,-0.13074,0.96929,135.69 > ui mousemode right ""move picked models"" > view matrix models > #4,0.96546,0.18607,-0.18237,-87.712,-0.15651,0.9738,0.16498,41.86,0.20829,-0.13074,0.96929,135.46 > view matrix models > #4,0.96546,0.18607,-0.18237,-85.578,-0.15651,0.9738,0.16498,38.781,0.20829,-0.13074,0.96929,137.13 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.94083,0.24764,-0.23132,-87.214,-0.197,0.95511,0.22124,39.847,0.27573,-0.16258,0.94739,137.33 > view matrix models > #4,0.94293,0.24291,-0.22775,-87.091,-0.19407,0.95671,0.2169,39.763,0.27058,-0.16032,0.94925,137.32 > view matrix models > #4,0.98444,0.12235,-0.1261,-83.807,-0.10904,0.9882,0.10758,37.765,0.13777,-0.092161,0.98617,136.76 > view matrix models > #4,-0.2608,0.057686,-0.96367,-115.51,0.91335,-0.30856,-0.26566,42.55,-0.31267,-0.94945,0.027786,112.17 > view matrix models > #4,-0.6873,-0.58226,-0.43427,-104.28,0.49988,0.054608,-0.86437,22.859,0.52701,-0.81116,0.25353,124.93 > view matrix models > #4,-0.094145,0.14375,-0.98513,-114.79,0.89513,-0.42089,-0.14696,45.672,-0.43576,-0.89565,-0.089048,108 > view matrix models > #4,-0.25112,0.063529,-0.96587,-115.49,0.91322,-0.31524,-0.25817,42.755,-0.32088,-0.94688,0.021148,111.93 > view matrix models > #4,-0.648,-0.35412,-0.67431,-110.57,0.72345,-0.0093688,-0.69031,29.39,0.23813,-0.93515,0.26226,122.92 > view matrix models > #4,0.087728,-0.75589,-0.6488,-101.78,0.81837,-0.31666,0.47958,59.912,-0.56796,-0.57303,0.59082,122.27 > view matrix models > #4,-0.26659,-0.80893,-0.52398,-101.81,0.89723,-0.40686,0.17162,53.426,-0.35201,-0.42438,0.83426,129.69 > view matrix models > #4,-0.60755,0.36193,0.70703,-78.933,0.48619,0.87336,-0.029296,40.296,-0.62809,0.32595,-0.70658,86.906 > view matrix models > #4,-0.64999,0.59008,0.47887,-85.688,0.65851,0.75186,-0.032642,42.221,-0.37931,0.29412,-0.87728,85.135 > view matrix models > #4,-0.62122,0.60071,0.50323,-84.865,0.6661,0.74305,-0.064716,41.538,-0.4128,0.295,-0.86173,85.204 > view matrix models > #4,-0.46323,0.64899,0.60352,-81.129,0.68141,0.69624,-0.22568,37.909,-0.56666,0.3067,-0.76474,86.117 > view matrix models > #4,-0.64319,0.59265,0.48484,-85.489,0.66047,0.74977,-0.040316,42.059,-0.38741,0.29429,-0.87368,85.148 > view matrix models > #4,-0.63571,0.59544,0.49124,-85.273,0.6625,0.74748,-0.048688,41.881,-0.39619,0.2945,-0.86966,85.165 > view matrix models > #4,-0.74021,0.55139,0.38478,-88.683,0.62075,0.78032,0.075946,44.428,-0.25837,0.29507,-0.91988,85.204 > view matrix models > #4,-0.82652,0.50219,0.25432,-92.494,0.55278,0.80943,0.19814,46.687,-0.10635,0.30435,-0.94661,85.918 > view matrix models > #4,-0.78393,0.52857,0.32567,-90.451,0.59182,0.79474,0.13469,45.547,-0.18763,0.29832,-0.93584,85.453 > view matrix models > #4,-0.68947,0.57427,0.44141,-86.912,0.64491,0.76414,0.013192,43.173,-0.32973,0.29377,-0.89721,85.106 > view matrix models > #4,-0.74019,0.55141,0.38481,-88.682,0.62077,0.78031,0.075916,44.428,-0.25841,0.29507,-0.91987,85.204 > view matrix models > #4,0.52789,0.34594,-0.77567,-104.65,-0.8045,0.49643,-0.32611,22.475,0.27225,0.79617,0.54036,124.03 > view matrix models > #4,0.069514,0.23518,-0.96946,-113.22,-0.77239,0.62771,0.096889,32.65,0.63133,0.74207,0.22528,119.82 > view matrix models > #4,-0.66525,0.58415,0.46499,-86.147,0.65372,0.75658,-0.015198,42.587,-0.36068,0.29386,-0.88519,85.114 > view matrix models > #4,-0.78943,0.52544,0.31736,-90.693,0.58748,0.7966,0.14247,45.691,-0.17795,0.29891,-0.93754,85.499 > view matrix models > #4,-0.67516,0.58018,0.45558,-86.455,0.6503,0.75967,-0.0036843,42.826,-0.34822,0.29377,-0.89019,85.107 > view matrix models > #4,-0.031842,0.99322,-0.1118,-95.829,0.97538,0.0553,0.21349,53.566,0.21822,-0.10225,-0.97053,89.729 > ui mousemode right ""move picked models"" > view matrix models > #4,-0.031842,0.99322,-0.1118,-101.54,0.97538,0.0553,0.21349,59.332,0.21822,-0.10225,-0.97053,88.087 > save C:/Users/Maciek/Desktop/FinO_proteins.cxs > transparncy 60 Unknown command: transparncy 60 > transparency 60 > open > F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/chimeraX/4_proteins.aln Summary of feedback from opening F:/Roboczy_folder/Projekt_domeny_FinO/FinO_proteins_strucural_analysis/chimeraX/4_proteins.aln --- notes | Alignment identifier is 4_proteins.aln Associated FopA chain A to FopA/1-200 with 0 mismatches Associated ProQ chain A to Ec_ProQ/1-232 with 0 mismatches Associated FinO chain A to Ec_FinO/1-186 with 1 mismatch Associated 3mw6 chain A to Nm_ProQ/1-141 with 3 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment 4_proteins.aln Opened 4 sequences from 4_proteins.aln > select #3/A:143 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:143 #1/A:157 #2/A:80 #4/A:87 70 atoms, 66 bonds, 4 residues, 4 models selected Seqview [ID: 4_proteins.aln] region Ec_FinO/1-186..Nm_ProQ/1-141 [161] RMSD: 103.636 > show sel atoms > color sel blue > save C:/Users/Maciek/Desktop/FinO_proteins.cxs > style sel sphere off Expected a keyword > style sel stick Changed 70 atom styles > select clear > save C:\Users\Maciek\Desktop\image1.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode C:\Users\Maciek\Desktop\movie1.mp4 Movie saved to \C:Users\\...\Desktop\movie1.mp4 > 2dlabels text ""concave side - ProQ R80 and homologous positions"" > view matrix models > #1,0.73395,0.10374,0.67124,-118.56,-0.072924,0.99459,-0.073976,-27.168,-0.67528,0.0053447,0.73754,44.176 > undo > ui mousemode right ""move label"" > 2dlabels #5.1 xpos 0.026 ypos 0.905 > save C:/Users/Maciek/Desktop/FinO_proteins.cxs ——— End of log from Tue Jul 20 15:35:07 2021 ——— opened ChimeraX session > ui tool show Rotamers > select #3/A:151@CA 1 atom, 1 residue, 1 model selected > select #3/A:151@CA 1 atom, 1 residue, 1 model selected > select #3/A:144@CE1 1 atom, 1 residue, 1 model selected > select #3/A:95@CB 1 atom, 1 residue, 1 model selected > select #3/A:144@CE1 1 atom, 1 residue, 1 model selected > select #3/A:95@CD1 1 atom, 1 residue, 1 model selected > select #3/A:144@CE1 1 atom, 1 residue, 1 model selected > select #3/A:143 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:143 #1/A:157 #2/A:80 #4/A:87 70 atoms, 66 bonds, 4 residues, 4 models selected Seqview [ID: 4_proteins.aln] region Ec_FinO/1-186..Nm_ProQ/1-141 [161] RMSD: 103.636 > style sel sticks Expected a keyword > hide sel atoms > show sel atoms > style sel stick Changed 70 atom styles > style sel stick Changed 70 atom styles > style sel ringFill off Changed 4 residue ring styles > select clear > select #3/A:143 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:143 #1/A:157 #2/A:80 #4/A:87 70 atoms, 66 bonds, 4 residues, 4 models selected Seqview [ID: 4_proteins.aln] region Ec_FinO/1-186..Nm_ProQ/1-141 [161] RMSD: 103.636 > style sel ball Changed 70 atom styles > style sel ball Changed 70 atom styles > style sel sphere Changed 70 atom styles > style sel sphere Changed 70 atom styles > style sel stick Changed 70 atom styles > hide sel @H Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel @hydrogens Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel @hydrogens atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide hydrogen Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide hydrogen atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide @hydrogen atoms > hide atoms @hydrogen Expected ',' or a keyword > hide atoms hydro Expected ',' or a keyword > delete H > save C:/Users/Maciek/Desktop/FinO_proteins.cxs ——— End of log from Wed Jul 21 14:22:07 2021 ——— opened ChimeraX session > delete 2dlabels Missing or invalid ""atoms"" argument: invalid atoms specifier > 2dlabels delete > mmaker #1 #2 #3 to #4 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 3mw6, chain A (#4) with FopA, chain A (#1), sequence alignment score = 139.1 RMSD between 47 pruned atom pairs is 1.091 angstroms; (across all 101 pairs: 7.497) Matchmaker 3mw6, chain A (#4) with ProQ, chain A (#2), sequence alignment score = 70.4 RMSD between 34 pruned atom pairs is 1.090 angstroms; (across all 101 pairs: 7.560) Matchmaker 3mw6, chain A (#4) with FinO, chain A (#3), sequence alignment score = 106.7 RMSD between 56 pruned atom pairs is 1.012 angstroms; (across all 97 pairs: 8.039) > select clear > hide surfaces > hide cartoons > undo > hide cartoons > select #3/A:143 #1/A:157 #2/A:80 #4/A:87 44 atoms, 40 bonds, 4 residues, 4 models selected > select #2/A:80 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:80 11 atoms, 10 bonds, 1 residue, 1 model selected > hide śel Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~sel > save C:/Users/Maciek/Desktop/FinO_proteins.cxs ——— End of log from Thu Jul 22 11:19:18 2021 ——— opened ChimeraX session OpenGL version: 3.3.0 - Build 27.20.100.8935 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Manufacturer: Dell Inc. Model: OptiPlex 7070 OS: Microsoft Windows 10 Pro (Build 19042) Memory: 8,361,283,584 MaxProcessMemory: 137,438,953,344 CPU: 6 Intel(R) Core(TM) i5-9500 CPU @ 3.00GHz OSLanguage: pl-PL Locale: ('pl_PL', 'cp1250') 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: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 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: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 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: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Structure Analysis can't reproduce Tom Goddard all ChimeraX