id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16438 Matchmaker: argument of type 'NoneType' is not iterable batu8991@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.9.dev202407111727 (2024-07-11 17:27:30 UTC) Description (Describe the actions that caused this problem to occur here) Matchmaker did not worked Log: UCSF ChimeraX version: 1.9.dev202407111727 (2024-07-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""C:\Users\altay\Desktop\gp66 my view.cxs"" format session Log from Mon Dec 9 16:31:14 2024UCSF ChimeraX version: 1.9.dev202407111727 (2024-07-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""C:\Users\altay\Desktop\Alphafold predictions interacting with > gp66\gp66_rainbow_xraycrystallography.cxs"" format session Log from Tue Sep 10 13:01:11 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif #1 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif #2 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif #3 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif #4 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif #5 --- Chain | Description A | . B | . > ui tool show AlphaFold > alphafold pae #1 file > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_full_data_1.json > color #1/B:341 lime > color #1/B:158 magenta > color #1/B:509-554 lime > color #1/B:351-422 magenta > color #1/B:671-676 lime > color #1/B:646-656 magenta > color #1/B:605-610 lime > color #1/B:839-849 magenta > ui tool show Matchmaker > matchmaker #2-5 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 fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif, chain B (#2), sequence alignment score = 11074.6 RMSD between 2051 pruned atom pairs is 0.478 angstroms; (across all 2180 pairs: 2.702) Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif, chain B (#3), sequence alignment score = 11085.7 RMSD between 2071 pruned atom pairs is 0.504 angstroms; (across all 2180 pairs: 3.689) Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif, chain B (#4), sequence alignment score = 11080.9 RMSD between 2039 pruned atom pairs is 0.657 angstroms; (across all 2180 pairs: 4.254) Matchmaker fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif, chain B (#1) with fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif, chain B (#5), sequence alignment score = 11088.7 RMSD between 2093 pruned atom pairs is 0.548 angstroms; (across all 2180 pairs: 3.525) > select #1/B 17455 atoms, 17778 bonds, 2180 residues, 1 model selected > select #1/A 2607 atoms, 2653 bonds, 331 residues, 1 model selected > split Split fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif (#1) into 3 models Split fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif (#2) into 3 models Split fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif (#3) into 3 models Split fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif (#4) into 3 models Split fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif (#5) into 3 models Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif A #1.1 --- Chain | Description A | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif B #1.2 --- Chain | Description B | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif A #2.1 --- Chain | Description A | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif B #2.2 --- Chain | Description B | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif A #3.1 --- Chain | Description A | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif B #3.2 --- Chain | Description B | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif A #4.1 --- Chain | Description A | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif B #4.2 --- Chain | Description B | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif A #5.1 --- Chain | Description A | No description available Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif B #5.2 --- Chain | Description B | No description available > hide #!1 models > hide #1.1 models > hide #1.2 models > hide #2.2 models > hide #2.1 models > hide #!2 models > hide #1.3 models > hide #!3 models > hide #2.3 models > hide #3.1 models > hide #3.2 models > hide #3.3 models > hide #!4 models > hide #4.1 models > hide #4.2 models > hide #4.3 models > hide #!5 models > show #!5 models > color #5.1 #8ffaf3ff > show #1.1 models > show #2.1 models > hide #2.1 models > show #4.1 models > show #3.1 models > show #2.1 models > hide #!2 models > show #!2 models > hide #5.3 models > show #5.3 models > rainbow #1.1#2.1#3.1#4.1#5.1-3 > undo > select add #5.2 17455 atoms, 17778 bonds, 2180 residues, 1 model selected > rainbow sel Alignment identifier is 5.2/B > select #5.2/B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5.2/B:1-19 152 atoms, 152 bonds, 19 residues, 1 model selected > select #5.2/B:2180 10 atoms, 9 bonds, 1 residue, 1 model selected > select #5.2/B:2162-2180 148 atoms, 147 bonds, 19 residues, 1 model selected > select #5.2/B:1681-2180 4040 atoms, 4109 bonds, 500 residues, 1 model selected > select #5.2/B:1877 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5.2/B:1877 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5.2/B:1848 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5.2/B:1848-1850 25 atoms, 24 bonds, 3 residues, 1 model selected > select #5.2/B:1835 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5.2/B:1835-1845 77 atoms, 76 bonds, 11 residues, 1 model selected > select #5.2/B:1840-1841 8 atoms, 7 bonds, 2 residues, 1 model selected > select #5.2/B:1840-1945 871 atoms, 890 bonds, 106 residues, 1 model selected > select #5.2/B:2013 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5.2/B:2013-2085 587 atoms, 596 bonds, 73 residues, 1 model selected > select > #5.2/B:18-27,30-40,43-49,106-126,130-132,140-162,165-179,181-195,201-213,224-226,229-232,235-243,268-279,294-308,310-321,324-334,372-387,390-392,396-415,424-445,452-459,471-494,505-508,510-524,548-558,560-568,572-574,576-581,596-609,624-626,635-650,694-720,723-725,747-749,756-758,765-771,789-816,839-844,853-879,882-884,888-899,931-940,945-956,969-978,984-994,1004-1006,1035-1038,1042-1052,1061-1063,1094-1096,1117-1124,1140-1166,1176-1189,1194-1201,1206-1208,1213-1229,1290-1295,1299-1301,1304-1310,1313-1316,1328-1330,1342-1344,1354-1358,1380-1392,1397-1406,1411-1413,1422-1434,1443-1450,1468-1470,1473-1488,1491-1498,1504-1514,1526-1528,1530-1560,1599-1614,1618-1621,1629-1637,1642-1649,1652-1665,1678-1690,1704-1713,1719-1743,1745-1748,1754-1772,1782-1785,1794-1812,1822-1834,1849-1866,1868-1870,1875-1891,1901-1904,1922-1938,1940-1954,1969-1974,1977-1990,1992-2005,2018-2020,2042-2044,2090-2092,2115-2130,2148-2151,2156-2161,2170-2172,2174-2176 8855 atoms, 8918 bonds, 1078 residues, 1 model selected > select #5.2/B:2112 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5.2/B:2112 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5.2/B:2114-2115 16 atoms, 15 bonds, 2 residues, 1 model selected > select #5.2/B:2114-2155 334 atoms, 338 bonds, 42 residues, 1 model selected > select #5.2/B:2050 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5.2/B:2050-2053 34 atoms, 33 bonds, 4 residues, 1 model selected > select #5.2/B:2109 11 atoms, 11 bonds, 1 residue, 1 model selected > select #5.2/B:2109-2133 206 atoms, 209 bonds, 25 residues, 1 model selected > open 6vr4 6vr4 title: Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2 [more info...] Chain information for 6vr4 #6 --- Chain | Description | UniProt A B | DNA-dependent RNA polymerase | S0A2C3_9CAUD 1-2180 Non-standard residues in 6vr4 #6 --- CL — chloride ion NA — sodium ion 6vr4 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > ui tool show Matchmaker > matchmaker #!6 to #1.1 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 fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif A, chain A (#1.1) with 6vr4, chain B (#6), sequence alignment score = 16.8 RMSD between 4 pruned atom pairs is 0.901 angstroms; (across all 21 pairs: 12.544) > ui tool show Matchmaker > matchmaker #5.2 to #6 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 6vr4, chain A (#6) with fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif B, chain B (#5.2), sequence alignment score = 10889.8 RMSD between 1752 pruned atom pairs is 0.898 angstroms; (across all 2166 pairs: 2.573) > select add #1 20269 atoms, 20640 bonds, 2537 residues, 5 models selected > select add #2 40332 atoms, 41071 bonds, 5049 residues, 9 models selected > select add #3 60395 atoms, 61502 bonds, 7561 residues, 13 models selected > select add #4 80458 atoms, 81933 bonds, 10073 residues, 17 models selected > select add #5.1 83065 atoms, 84586 bonds, 10404 residues, 18 models selected > select add #5.3 83066 atoms, 84586 bonds, 10405 residues, 19 models selected > delete Missing or invalid ""atoms"" argument: empty atom specifier > close session > open > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_1.cif #1 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_2.cif #2 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_3.cif #3 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_4.cif #4 --- Chain | Description A | . B | . Chain information for fold_gene2_and_gp66_2024_09_05_13_42_model_0.cif #5 --- Chain | Description A | . B | . > close session > open 6vr4 6vr4 title: Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2 [more info...] Chain information for 6vr4 #1 --- Chain | Description | UniProt A B | DNA-dependent RNA polymerase | S0A2C3_9CAUD 1-2180 Non-standard residues in 6vr4 #1 --- CL — chloride ion NA — sodium ion 6vr4 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select /A 17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected > split Split 6vr4 (#1) into 2 models Chain information for 6vr4 A #1.1 --- Chain | Description A | No description available Chain information for 6vr4 B #1.2 --- Chain | Description B | No description available > select add #1.1 17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected > rainbow sel > hide #!1.1 models > show #!1.1 models > select add #1 34715 atoms, 35334 bonds, 2 pseudobonds, 4359 residues, 5 models selected > select subtract #1 Nothing selected Alignment identifier is 1 > select #1.1/A:1361 #1.2/B:1361 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1.1/A:1361-1365 #1.2/B:1361-1365 86 atoms, 86 bonds, 10 residues, 2 models selected 1 [ID: 1] region chains A,B [1360-1364] RMSD: 67.152 > delete /B > save > C:/Users/altay/Downloads/fold_gene2_and_gp66_2024_09_05_13_42/gp66_rainbow_cryoEM.cxs ——— End of log from Tue Sep 10 13:01:11 2024 ——— opened ChimeraX session > cartoon style sel xsection oval modeHelix default > show sel cartoons > color sel bypolymer > color #1.1 #ffaaffff > select add #1.1 17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected > select subtract #1.1 Nothing selected > select add #1.1 17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 2 models selected > cartoon style (#!1.1 & sel) modeHelix tube sides 20 > cartoon style (#!1.1 & sel & coil) xsection oval > cartoon style (#!1.1 & sel) xsection barbell modeHelix default > cartoon style (#!1.1 & sel) xsection rectangle modeHelix default > cartoon style (#!1.1 & sel) xsection oval modeHelix default > cartoon style (#!1.1 & sel & coil) xsection oval > cartoon style (#!1.1 & sel) xsection barbell modeHelix default No Surface models open [Repeated 1 time(s)] > select subtract #1.1 Nothing selected > select clear > select /A:211 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:200 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:200-216 129 atoms, 128 bonds, 17 residues, 1 model selected > color sel cyan > select /A:902 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:902-1011 879 atoms, 895 bonds, 110 residues, 1 model selected > color sel orange > color sel blue > select /A:1269 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:1269-1311 337 atoms, 342 bonds, 43 residues, 1 model selected > select /A:1232 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:1232-1371 1076 atoms, 1097 bonds, 140 residues, 1 model selected > color sel orange > view orient > undo > select > /A:17-50,105-125,139-162,164-196,200-215,217-221,223-243,267-280,293-309,312-321,323-335,371-393,395-417,423-445,451-461,471-495,504-509,513-523,547-583,595-610,634-651,693-726,746-750,755-772,788-817,838-843,852-878,881-885,887-900,930-939,944-956,968-979,983-995,1001-1007,1034-1039,1043-1053,1116-1125,1139-1167,1175-1191,1193-1202,1205-1209,1212-1229,1289-1296,1303-1315,1327-1331,1341-1345,1353-1359,1379-1393,1396-1404,1413-1418,1422-1434,1442-1451,1467-1499,1504-1515,1525-1560,1598-1612,1618-1623,1628-1639,1641-1665,1677-1691,1703-1713,1718-1742,1753-1773,1781-1785,1793-1813,1821-1834,1848-1871,1874-1895,1900-1905,1921-1955,1963-2006,2017-2021,2090-2093,2111-2128,2130-2134,2146-2153,2155-2162 9909 atoms, 10011 bonds, 1222 residues, 1 model selected Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\cmd_line\tool.py"", line 319, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3174, in run self.log_parse_error() File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3301, in log_parse_error text_color, err_color, ^^^^^^^^^^ NameError: name 'text_color' is not defined NameError: name 'text_color' is not defined File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3301, in log_parse_error text_color, err_color, ^^^^^^^^^^ See log for complete Python traceback. > save myview Cannot determine format for 'myview' > save ""C:/Users/altay/Desktop/gp66 my view.cxs"" ——— End of log from Mon Dec 9 16:31:14 2024 ——— opened ChimeraX session > select add #1 17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 3 models selected > select subtract #1 Nothing selected > select /A:842 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:842-1120 2191 atoms, 2231 bonds, 279 residues, 1 model selected > ui tool show ""Color Actions"" > color sel hot pink > color sel pale violet red [Repeated 1 time(s)] > color sel purple > color sel blue > color sel chartreuse > undo [Repeated 5 time(s)] > color sel bypolymer > select /A:902 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:902-1101 1558 atoms, 1584 bonds, 200 residues, 1 model selected > select /A:1101 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:1101-1102 17 atoms, 16 bonds, 2 residues, 1 model selected > select /A:1103 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:902-1103 1574 atoms, 1600 bonds, 202 residues, 1 model selected > color sel blue > select /A:1361 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1361 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1363 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1363 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1365 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1365 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1361 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1361 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1363 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1365 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1365 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1:1361,1363,1365 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > cartoon style (sel & coil) xsection oval > cartoon style sel xsection barbell modeHelix default > select add #1 17359 atoms, 17667 bonds, 1 pseudobond, 2181 residues, 3 models selected > cartoon style (#!1.1 & sel & coil) xsection oval > cartoon style (#!1.1 & sel) xsection barbell modeHelix default > cartoon style (#!1.1 & sel) xsection rectangle modeHelix default > cartoon style (#!1.1 & sel) xsection oval modeHelix default > lighting flat > select subtract #1 Nothing selected > lighting flat > lighting soft > lighting full > lighting simple > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting soft > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > set bgColor white > select #1:1361,1363,1365 24 atoms, 21 bonds, 3 residues, 1 model selected > style sel stick Changed 24 atom styles > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54, maximum 10.26 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54, maximum 10.26 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54, maximum 10.26 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for 6vr4 A_A SES surface #1.1.2: minimum, -32.72, mean -4.54, maximum 10.26 To also show corresponding color key, enter the above coulombic command and add key true > color bfactor sel 24 atoms, 3 residues, 1 surfaces, atom bfactor range 54.2 to 128 > undo [Repeated 5 time(s)] > hide sel atoms > hide sel cartoons > hide sel surfaces > show sel cartoons > show sel atoms > style sel stick Changed 24 atom styles > color sel byhetero > color bfactor sel 24 atoms, 3 residues, 1 surfaces, atom bfactor range 54.2 to 128 > color (#!1.1 & sel) red > view orient > open C:/Users/altay/Downloads/fold_gene50_and_gp66.zip Unrecognized file suffix '.zip' > save ""C:/Users/altay/Downloads/fold_gene50_and_gp66 (1)/gp66 my view.cxs"" > open ""C:/Users/altay/Downloads/fold_gene50_and_gp66 > (1)/fold_gene50_and_gp66_model_4.cif"" > ""C:/Users/altay/Downloads/fold_gene50_and_gp66 > (1)/fold_gene50_and_gp66_model_0.cif"" > ""C:/Users/altay/Downloads/fold_gene50_and_gp66 > (1)/fold_gene50_and_gp66_model_1.cif"" > ""C:/Users/altay/Downloads/fold_gene50_and_gp66 > (1)/fold_gene50_and_gp66_model_2.cif"" > ""C:/Users/altay/Downloads/fold_gene50_and_gp66 > (1)/fold_gene50_and_gp66_model_3.cif"" Chain information for fold_gene50_and_gp66_model_4.cif #2 --- Chain | Description A | . B | . Chain information for fold_gene50_and_gp66_model_0.cif #3 --- Chain | Description A | . B | . Chain information for fold_gene50_and_gp66_model_1.cif #4 --- Chain | Description A | . B | . Chain information for fold_gene50_and_gp66_model_2.cif #5 --- Chain | Description A | . B | . Chain information for fold_gene50_and_gp66_model_3.cif #6 --- Chain | Description A | . B | . > ui tool show Matchmaker Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1284, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\match_maker\\__init__.py"", line 44, in start_tool return MatchMakerTool(session, tool_name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\match_maker\tool.py"", line 166, in __init__ self._match_value_change() File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\match_maker\tool.py"", line 366, in _match_value_change match_value = match_widget.value ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 130, in value return self.get_value() ^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 133, in get_value self._sleep_check() File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 89, in _sleep_check self._items_change() File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 169, in _items_change item_names = self._item_names() # updates things ^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 47, in _item_names values = [v for v in self.list_func() if self.filter_func(v)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 47, in values = [v for v in self.list_func() if self.filter_func(v)] ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 22, in filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and isinstance(x, cf) ^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\match_maker\tool.py"", line 60, in filter_func=lambda s, ref_list=self.ref_structure_list: s != ref_list.value) ^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 130, in value return self.get_value() ^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 133, in get_value self._sleep_check() File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 89, in _sleep_check self._items_change() File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 172, in _items_change filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in prev_value] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 172, in filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in prev_value] ^^^^^^^^^^^^^^^ TypeError: argument of type 'NoneType' is not iterable During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1853, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\cmd.py"", line 219, in ui_tool_show return bi.start_tool(session, name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker in bundle ChimeraX-MatchMaker: argument of type 'NoneType' is not iterable chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker in bundle ChimeraX-MatchMaker: argument of type 'NoneType' is not iterable File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\core\toolshed\info.py"", line 578, in start_tool raise ToolshedError( See log for complete Python traceback. > ui tool show Matchmaker Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 79, in showEvent self._items_change() File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 172, in _items_change filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in prev_value] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 172, in filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in prev_value] ^^^^^^^^^^^^^^^ TypeError: argument of type 'NoneType' is not iterable TypeError: argument of type 'NoneType' is not iterable File ""C:\Program Files\ChimeraX 1.9.dev202407111727\bin\Lib\site- packages\chimerax\ui\widgets\item_chooser.py"", line 172, in filtered_sel = [self.value_map[v] for v in self.value_map.keys() if v in prev_value] ^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 31.0.101.4953 OpenGL renderer: Intel(R) UHD Graphics 770 OpenGL vendor: Intel Python: 3.11.4 Locale: de_DE.cp1252 Qt version: PyQt6 6.7.0, Qt 6.7.1 Qt runtime version: 6.7.2 Qt platform: windows Manufacturer: Dell Inc. Model: OptiPlex Micro Plus 7020 OS: Microsoft Windows 11 Enterprise (Build 22631) Memory: 34,031,325,184 MaxProcessMemory: 137,438,953,344 CPU: 32 Intel(R) Core(TM) i9-14900 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: 2024.7.4 cftime: 1.6.4 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: 2.13 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.3 ChimeraX-AtomicLibrary: 14.1.1 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: 2.13 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 1.0.5 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: 1.9.dev202407111727 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-DeepMutationalScan: 1.0 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-Foldseek: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.2 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.3 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: 1.1.7 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: 2.1.5 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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: 1.13.5 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 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: 1.3 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: 3.1.5 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.12.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.3 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: 1.17 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.6 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.8.2 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.1 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: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.3 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.11 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: 2.10.1 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.1 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: 3.0.47 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: 6.7.0 PyQt6-Qt6: 6.7.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.2 PyQt6-WebEngineSubwheel-Qt6: 6.7.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.2 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.32.3 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: 6.4.1 traitlets: 5.14.2 typing_extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.2 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 WMI: 1.5.1 }}} " defect closed normal General Controls duplicate all ChimeraX