id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15299 No blast results keth105@… Zach Pearson "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.8rc202405230136 (2024-05-23 01:36:41 UTC) Description 1. The blast protein result does not show up. 2. I cannot input sequenecs in Modeller Comparative. Log: Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405230136 (2024-05-23) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ""Blast Protein"" > blastprotein > LDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp1 Webservices job id: CI8N4Z5TXL10287I > showResultsTable Unknown command: showResultsTable > ui dockable true ""Blast Protein"" > help help:user/preferences.html#window > ui tool show ""Show Sequence Viewer"" > buttonpanel Missing or invalid ""title"" argument: Expected a text string > buttonpanel blastprotein > buttonpanel blastprotein add Missing ""add"" keyword's argument > buttonpanel blastprotein add showResultsTable No command specified for button ""showResultsTable"" > buttonpanel blastprotein add showResults No command specified for button ""showResults"" > buttonpanel blastprotein add Results No command specified for button ""Results"" > buttonpanel blastprotein add name No command specified for button ""name"" > buttonpanel blastprotein add results No command specified for button ""results"" > open blastprotein results 'blastprotein' has no suffix > buttonpanel showResultsTable > help help:devel > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > open lgcn 'lgcn' has no suffix > open CI8N4Z5TXL10287I.html No such file/path: CI8N4Z5TXL10287I.html > open 1gcn Summary of feedback from opening 1gcn fetched from pdb --- note | Fetching compressed mmCIF 1gcn from http://files.rcsb.org/download/1gcn.cif 1gcn title: X-ray analysis of glucagon and its relationship to receptor binding [more info...] Chain information for 1gcn #1 --- Chain | Description | UniProt A | GLUCAGON | GLUC_PIG 1-29 > open Blast Results 'Blast' has no suffix > blastprotein > >EVD68LDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp2 Missing or invalid ""atoms"" argument: Expected an atom specifier, [alignment- id:]sequence-name-or-number, or sequence > blastprotein > >EVD68_VPLDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp3 Missing or invalid ""atoms"" argument: Expected an atom specifier, [alignment- id:]sequence-name-or-number, or sequence > blastprotein > LDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ > database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp4 Webservices job id: M7CNAEM2H6BPQMFG > buttonpanel Blast Protein Results Expected a keyword > open 4WM8 format mmcif fromDatabase pdb 4wm8 title: Crystal Structure of Human Enterovirus D68 [more info...] Chain information for 4wm8 #2 --- Chain | Description | UniProt A | VP1 | Q9YLJ3_9ENTO 1-297 B | VP2 | Q68T42_9ENTO 1-248 C | VP3 | Q68T42_9ENTO 1-247 D | VP4 | Q8QWD4_9ENTO 1-68 Non-standard residues in 4wm8 #2 --- DKA — decanoic acid 4wm8 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 > version None name bp5 Webservices job id: MJRQ27QLX7EIP7IH > blastprotein #2/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 > version None name bp6 Webservices job id: TNVAAZ94REPH0WI9 > blastprotein #2/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 > version None name bp7 Webservices job id: 7F2COE2MXEC000HE > ui tool show ""Modeller Comparative"" > close #1 > close #2 > open 6CV2 format mmcif fromDatabase pdb 6cv2 title: CryoEM structure of human enterovirus D68 full virion [more info...] Chain information for 6cv2 #1 --- Chain | Description | UniProt A | viral protein 1 | A0A0X7Z9B1_9ENTO 1-297 B | viral protein 3 | E9RIT6_9ENTO 1-247 C | viral protein 2 | A0A097ZN88_9ENTO 1-248 D | viral protein 4 | A0A0P0DH17_9ENTO 1-68 6cv2 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > color bychain > ui tool show ""Modeller Comparative"" No alignments chosen for modeling > open C:/Users/philip/Downloads/cryosparc_P4_J35_011_volume_map_sharp.mrc Opened cryosparc_P4_J35_011_volume_map_sharp.mrc as #2, grid size 1080,1080,1080, pixel 0.478, shown at step 1, values float32 > hide #!1 models > volume #2 region 0,0,0,1079,1079,1079 step 8 [Repeated 1 time(s)] > volume #2 change image level -0.01043,0 level 0.059,0.8 level 0.183,1 > volume #2 level 0.03678 > view > volume #2 level 0.02292 > volume #2 level 0.01509 > surface dust #2 size 4.78 > volume #2 step 1 > volume #2 level 0.01984 > view orient > volume #2 transparency 0.5 > lighting soft > show #!1 models > select add #1 6306 atoms, 6467 bonds, 1 pseudobond, 810 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,250.06,0,1,0,80.311,0,0,1,0 > sym #1 assembly 3 Made 5 copies for 6cv2 assembly 3 > view > select subtract #1 Nothing selected > select add #3 31530 atoms, 32335 bonds, 5 pseudobonds, 4050 residues, 11 models selected > view matrix models #3,1,0,0,296.25,0,1,0,86.381,0,0,1,0 > view matrix models > #3,0.97915,0.20316,0,249.8,-0.20316,0.97915,0,141.31,0,0,1,0 > view matrix models > #3,0.97025,0.24209,0,241.93,-0.24209,0.97025,0,153.21,0,0,1,0 > view matrix models > #3,0.97025,0.24209,0,-43.792,-0.24209,0.97025,0,155.94,0,0,1,14.749 > view matrix models > #3,0.97185,0.22575,-0.067367,-14.568,-0.21236,0.96328,0.16432,88.759,0.10199,-0.14538,0.9841,33.098 > view matrix models > #3,0.97185,0.22575,-0.067367,-18.655,-0.21236,0.96328,0.16432,93.335,0.10199,-0.14538,0.9841,30.912 > view matrix models > #3,0.96614,0.21648,-0.1404,12.753,-0.1795,0.95479,0.23697,60.252,0.18535,-0.20374,0.96132,34.152 > view matrix models > #3,0.96927,0.24561,0.014185,-53.992,-0.24349,0.94945,0.19812,92.404,0.035191,-0.19549,0.98008,62.376 > view matrix models > #3,0.97031,0.24188,-0.0004654,-47.774,-0.19807,0.79568,0.57242,-20.012,0.13883,-0.55533,0.81996,189.85 > view matrix models > #3,0.97031,0.24188,-0.0004654,-45.776,-0.19807,0.79568,0.57242,-34.518,0.13883,-0.55533,0.81996,179.62 > view [Repeated 1 time(s)] > view matrix models > #3,0.97031,0.24188,-0.0004654,-47.284,-0.19807,0.79568,0.57242,-34.651,0.13883,-0.55533,0.81996,179.61 > view matrix models > #3,0.97031,0.24188,-0.0004654,-48.491,-0.19807,0.79568,0.57242,-24.643,0.13883,-0.55533,0.81996,169.84 > ui tool show ""Fit in Map"" > select subtract #3 Nothing selected > select add #3.1 6306 atoms, 6467 bonds, 1 pseudobond, 810 residues, 2 models selected > fitmap #3.1 inMap #2 Fit molecule 6cv2 (#3.1) to map cryosparc_P4_J35_011_volume_map_sharp.mrc (#2) using 6306 atoms average map value = 0.01988, steps = 224 shifted from previous position = 4.18 rotated from previous position = 7.4 degrees atoms outside contour = 3863, contour level = 0.019837 Position of 6cv2 (#3.1) relative to cryosparc_P4_J35_011_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99770900 -0.05716541 0.03617830 0.02849675 0.05284863 0.99244463 0.11072799 -57.77560021 -0.04223477 -0.10856234 0.99319205 36.96309354 Axis -0.85139661 0.30443944 0.42713048 Axis point 0.00000000 313.91052472 538.18007417 Rotation angle (degrees) 7.39925549 Shift along axis -1.82536986 Opened 6cv2 map 2.88 as #4, grid size 108,108,91, pixel 0.96, shown at level 0.113, step 1, values float32 > fitmap #3.1 inMap #2 resolution 2.88 Fit map 6cv2 map 2.88 in map cryosparc_P4_J35_011_volume_map_sharp.mrc using 71670 points correlation = 0.3741, correlation about mean = 0.01366, overlap = 764.4 steps = 212, shift = 14.2, angle = 13.5 degrees Position of 6cv2 map 2.88 (#4) relative to cryosparc_P4_J35_011_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99784847 -0.02712567 -0.05968779 36.56114623 0.02092472 0.99454727 -0.10216596 21.97705123 0.06213365 0.10069720 0.99297507 -32.08750743 Axis 0.84015344 -0.50452089 0.19899970 Axis point 0.00000000 363.04345103 261.13579516 Rotation angle (degrees) 6.93422496 Shift along axis 13.24368702 Average map value = 0.005242 for 6306 atoms, 5468 outside contour > undo [Repeated 2 time(s)] > sym #1 assembly 3 Made 5 copies for 6cv2 assembly 3 > view > select subtract #3 Nothing selected > select add #5 31530 atoms, 32335 bonds, 5 pseudobonds, 4050 residues, 11 models selected > view matrix models #5,1,0,0,8.0429,0,1,0,-54.131,0,0,1,17.34 > view matrix models #5,1,0,0,-65.515,0,1,0,-139.63,0,0,1,-23.269 > view matrix models > #5,0.92491,-0.27768,-0.25968,119.21,-0.18406,0.27061,-0.94493,440.51,0.33266,0.92177,0.19918,-34.925 > view matrix models > #5,0.90747,-0.23786,-0.34629,146.4,-0.22577,0.41903,-0.87946,390.02,0.35429,0.87626,0.32656,-77.052 > view matrix models > #5,0.90747,-0.23786,-0.34629,134.22,-0.22577,0.41903,-0.87946,371.79,0.35429,0.87626,0.32656,-167.56 > view matrix models > #5,0.85178,-0.37228,-0.36861,188.89,-0.38282,0.038038,-0.92304,518.93,0.35765,0.92734,-0.11012,-16.269 > view matrix models > #5,0.86986,-0.34935,-0.34828,171.29,-0.34042,0.085836,-0.93635,501.92,0.357,0.93305,-0.04426,-42.139 > view matrix models > #5,0.86986,-0.34935,-0.34828,201.61,-0.34042,0.085836,-0.93635,515.45,0.357,0.93305,-0.04426,-46.064 > view matrix models > #5,0.78169,-0.34162,-0.52179,286.58,-0.49993,0.15697,-0.85172,505.66,0.37287,0.92664,-0.048082,-46.974 > view matrix models > #5,0.78482,-0.3879,-0.48331,282.71,-0.50477,0.052326,-0.86167,535.76,0.35953,0.92022,-0.15473,-2.2067 > view matrix models > #5,0.79827,-0.35979,-0.48302,272.35,-0.48104,0.10174,-0.87078,521.56,0.36244,0.92747,-0.091861,-27.393 > view matrix models > #5,0.79827,-0.35979,-0.48302,262.53,-0.48104,0.10174,-0.87078,526.67,0.36244,0.92747,-0.091861,-34.101 > view matrix models > #5,0.79827,-0.35979,-0.48302,285.27,-0.48104,0.10174,-0.87078,580.34,0.36244,0.92747,-0.091861,-89.269 > view matrix models > #5,0.79827,-0.35979,-0.48302,239.75,-0.48104,0.10174,-0.87078,553.31,0.36244,0.92747,-0.091861,-68.548 > view matrix models > #5,0.81383,-0.10958,-0.57068,207.46,-0.55906,0.12026,-0.82036,548.85,0.15853,0.98668,0.036612,-81.427 > view matrix models > #5,0.83283,0.023957,-0.553,163.13,-0.54116,0.24522,-0.80437,507.54,0.11634,0.96917,0.21719,-135.09 > view matrix models > #5,0.83283,0.023957,-0.553,152.02,-0.54116,0.24522,-0.80437,499.77,0.11634,0.96917,0.21719,-124.6 > view matrix models > #5,0.82628,-0.060703,-0.55998,177.3,-0.55146,0.11524,-0.8262,542.88,0.11469,0.99148,0.061746,-70.866 > view matrix models > #5,0.82628,-0.060703,-0.55998,183.57,-0.55146,0.11524,-0.8262,549.16,0.11469,0.99148,0.061746,-78.19 > view matrix models > #5,0.66398,-0.45458,-0.59371,334.31,-0.61849,0.11236,-0.77772,548.27,0.42025,0.88359,-0.20655,-26.02 > view matrix models > #5,0.66398,-0.45458,-0.59371,333,-0.61849,0.11236,-0.77772,549.41,0.42025,0.88359,-0.20655,-28.359 > view matrix models > #5,0.66562,-0.43867,-0.60375,332.69,-0.63431,0.093681,-0.76738,554.22,0.39319,0.89375,-0.2159,-20.634 > view matrix models > #5,0.66562,-0.43867,-0.60375,342.21,-0.63431,0.093681,-0.76738,572.76,0.39319,0.89375,-0.2159,-16.856 > view matrix models > #5,0.77245,-0.16262,-0.6139,251.94,-0.62919,-0.06466,-0.77456,613.14,0.086267,0.98457,-0.15227,12.393 > view matrix models > #5,0.77245,-0.16262,-0.6139,243.81,-0.62919,-0.06466,-0.77456,620.23,0.086267,0.98457,-0.15227,24.87 > view matrix models > #5,0.77245,-0.16262,-0.6139,271.15,-0.62919,-0.06466,-0.77456,645.95,0.086267,0.98457,-0.15227,34.059 > view matrix models > #5,0.77245,-0.16262,-0.6139,250.88,-0.62919,-0.06466,-0.77456,617.56,0.086267,0.98457,-0.15227,18.894 > view matrix models > #5,0.77245,-0.16262,-0.6139,248.88,-0.62919,-0.06466,-0.77456,613.09,0.086267,0.98457,-0.15227,26.657 > view matrix models > #5,0.6499,-0.10131,-0.75323,316.69,-0.75969,-0.11561,-0.63993,606.4,-0.022256,0.98811,-0.1521,52.104 > view matrix models > #5,0.6499,-0.10131,-0.75323,315.1,-0.75969,-0.11561,-0.63993,602.25,-0.022256,0.98811,-0.1521,53.893 > view matrix models > #5,0.6499,-0.10131,-0.75323,320.99,-0.75969,-0.11561,-0.63993,608.55,-0.022256,0.98811,-0.1521,63.319 > view matrix models > #5,0.6499,-0.10131,-0.75323,323.11,-0.75969,-0.11561,-0.63993,607.62,-0.022256,0.98811,-0.1521,60.598 > view matrix models > #5,0.4391,-0.47611,-0.76191,470.29,-0.79222,0.19481,-0.5783,515.87,0.42376,0.85754,-0.29164,35.163 > view matrix models > #5,0.4187,-0.5603,-0.71467,478.06,-0.79793,0.14876,-0.58411,530.6,0.43359,0.81482,-0.38479,77.883 > view matrix models > #5,0.43148,-0.45659,-0.77804,473.43,-0.78818,0.22876,-0.57135,504.04,0.43885,0.85977,-0.26117,19.438 > view matrix models > #5,0.42668,-0.44601,-0.78677,475.35,-0.78717,0.24519,-0.5659,497.81,0.44531,0.86079,-0.24647,12.122 > view matrix models > #5,0.42668,-0.44601,-0.78677,453.85,-0.78717,0.24519,-0.5659,491.02,0.44531,0.86079,-0.24647,-0.14224 > view matrix models > #5,0.44144,-0.43522,-0.78467,446.81,-0.79081,0.22448,-0.56941,498.25,0.42396,0.87189,-0.24508,1.9318 > view matrix models > #5,0.37503,-0.47593,-0.79551,477.15,-0.76527,0.32537,-0.55543,462.25,0.52318,0.81708,-0.24219,-10.329 > view matrix models > #5,0.37503,-0.47593,-0.79551,485.76,-0.76527,0.32537,-0.55543,476.99,0.52318,0.81708,-0.24219,-5.8051 > view matrix models > #5,0.34122,-0.59426,-0.7283,497.99,-0.78594,0.24464,-0.56785,506.66,0.51562,0.76616,-0.38357,61.801 > view matrix models > #5,0.35855,-0.52508,-0.77184,491.62,-0.77184,0.29831,-0.56149,486.39,0.52508,0.79706,-0.29831,18.958 > view matrix models > #5,0.11573,-0.70853,-0.69612,569,-0.62544,0.49247,-0.60523,416.36,0.77165,0.50543,-0.38615,63.545 > view matrix models > #5,0.071503,-0.71689,-0.69351,581.48,-0.58554,0.53271,-0.61103,398.17,0.80748,0.44977,-0.38168,67.109 > view matrix models > #5,0.071503,-0.71689,-0.69351,587.62,-0.58554,0.53271,-0.61103,402.8,0.80748,0.44977,-0.38168,70.529 > view matrix models > #5,0.071503,-0.71689,-0.69351,589.55,-0.58554,0.53271,-0.61103,393.84,0.80748,0.44977,-0.38168,62.441 > view matrix models > #5,0.071503,-0.71689,-0.69351,592.48,-0.58554,0.53271,-0.61103,396.83,0.80748,0.44977,-0.38168,62.21 > view matrix models > #5,0.07163,-0.70258,-0.70799,594.38,-0.57573,0.5505,-0.60455,387.31,0.81449,0.45092,-0.36507,53.741 > view matrix models > #5,0.049082,-0.76318,-0.64432,591.14,-0.61946,0.48277,-0.61903,420.91,0.78349,0.42951,-0.44907,98.775 > view matrix models > #5,0.15332,-0.74312,-0.65135,560.39,-0.73556,0.35434,-0.57741,466.43,0.65989,0.56764,-0.49228,110.23 > view matrix models > #5,0.24022,-0.65449,-0.71689,540.7,-0.65516,0.43563,-0.61725,440.49,0.71628,0.61796,-0.32415,19.206 > view matrix models > #5,0.23211,-0.62622,-0.74429,544.15,-0.73119,0.39231,-0.55809,449.6,0.64148,0.67375,-0.36683,39.866 > view matrix models > #5,0.3619,-0.63302,-0.68434,490.06,-0.51976,0.47239,-0.71183,433.57,0.77387,0.6133,-0.15806,-58.354 > view matrix models > #5,0.3619,-0.63302,-0.68434,363.13,-0.51976,0.47239,-0.71183,474.07,0.77387,0.6133,-0.15806,-80.352 > view matrix models > #5,0.3619,-0.63302,-0.68434,518.08,-0.51976,0.47239,-0.71183,429.04,0.77387,0.6133,-0.15806,-24.14 > view > view matrix models > #5,0.3619,-0.63302,-0.68434,509.77,-0.51976,0.47239,-0.71183,418.36,0.77387,0.6133,-0.15806,-31.109 > view matrix models > #5,0.40187,-0.56565,-0.7201,496.13,-0.48358,0.53669,-0.69146,385.18,0.7776,0.6261,-0.057859,-73.257 > view matrix models > #5,0.57498,-0.53547,-0.6186,406.1,-0.3836,0.49138,-0.78191,404.86,0.72266,0.68688,0.077129,-125.09 > view matrix models > #5,0.66134,-0.59533,-0.4563,337.71,-0.34663,0.29691,-0.88977,483.69,0.66519,0.74661,-0.010003,-92.334 > view matrix models > #5,0.77086,-0.51793,-0.37084,258.76,-0.33597,0.16403,-0.92748,527.59,0.5412,0.83955,-0.047565,-69.238 > view matrix models > #5,0.79709,-0.45616,-0.39569,246.43,-0.34562,0.19271,-0.91838,519.67,0.49518,0.86878,-0.0040522,-81.111 > view matrix models > #5,0.80758,-0.48312,-0.33825,228.83,-0.33328,0.099328,-0.93758,546.47,0.48657,0.8699,-0.080798,-50.349 > view matrix models > #5,0.75587,-0.41623,-0.50539,288.26,-0.41852,0.28644,-0.86186,493.88,0.5035,0.86296,0.042313,-99.146 > view matrix models > #5,0.75587,-0.41623,-0.50539,270.72,-0.41852,0.28644,-0.86186,499.77,0.5035,0.86296,0.042313,-83.473 > view matrix models > #5,0.75587,-0.41623,-0.50539,260.79,-0.41852,0.28644,-0.86186,503.9,0.5035,0.86296,0.042313,-85.678 > view matrix models > #5,0.75587,-0.41623,-0.50539,262.05,-0.41852,0.28644,-0.86186,507.27,0.5035,0.86296,0.042313,-85.003 [Repeated 1 time(s)] > view matrix models > #5,0.82111,-0.24912,-0.51353,208.49,-0.43073,0.31987,-0.84389,495.44,0.37449,0.91412,0.15535,-107.99 > view matrix models > #5,0.82111,-0.24912,-0.51353,214.97,-0.43073,0.31987,-0.84389,537.19,0.37449,0.91412,0.15535,-87.52 > view matrix models > #5,0.82111,-0.24912,-0.51353,220.06,-0.43073,0.31987,-0.84389,539.38,0.37449,0.91412,0.15535,-47.4 > view matrix models > #5,0.82111,-0.24912,-0.51353,255.91,-0.43073,0.31987,-0.84389,495.85,0.37449,0.91412,0.15535,-117.57 > view matrix models > #5,0.82111,-0.24912,-0.51353,232.78,-0.43073,0.31987,-0.84389,475.04,0.37449,0.91412,0.15535,-117.16 > select subtract #5 Nothing selected > select add #5.1 6306 atoms, 6467 bonds, 1 pseudobond, 810 residues, 2 models selected > fitmap #5.1 inMap #2 resolution 2.88 Fit map 6cv2 map 2.88 in map cryosparc_P4_J35_011_volume_map_sharp.mrc using 71670 points correlation = 0.3706, correlation about mean = 0.02138, overlap = 770.5 steps = 276, shift = 13.8, angle = 16.8 degrees Position of 6cv2 map 2.88 (#4) relative to cryosparc_P4_J35_011_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.96265766 0.25885268 -0.07928125 -11.77238088 -0.24900659 0.96154095 0.11590822 32.36639267 0.10623532 -0.09183838 0.99009079 4.34369993 Axis -0.35866598 -0.32028675 -0.87679822 Axis point 105.67164200 74.51385092 0.00000000 Rotation angle (degrees) 16.83461604 Shift along axis -9.95272253 Average map value = 0.01352 for 6306 atoms, 4562 outside contour > Help....report a bug Unknown command: Help....report a bug > Help... balst protein results does not show up Unknown command: Help... balst protein results does not show up > Help... Unknown command: Help... > Help... Report a Bug Unknown command: Help... Report a Bug > Help...Report a Bug Unknown command: Help...Report a Bug > ui dockable true ""Volume Viewer"" > ui tool show ""Blast Protein"" > blastprotein #3.2/B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 > version None name bp8 Webservices job id: QANA1WHY03YLG1QI > ui tool show ""Modeller Comparative"" OpenGL version: 3.3.0 NVIDIA 536.23 OpenGL renderer: NVIDIA GeForce RTX 2080 SUPER/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: ASUS Model: System Product Name OS: Microsoft Windows 10 Pro (Build 19045) Memory: 68,527,972,352 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.2.2 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.4 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202405230136 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.1 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.0 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 WMI: 1.5.1 }}} " defect closed blocker 1.8 Sequence fixed Eric Pettersen Greg Couch all ChimeraX