id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14460 glDrawBuffer: invalid operation chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-6.5.0-14-generic-x86_64-with-glibc2.38 ChimeraX Version: 1.7rc202311220128 (2023-11-22 01:28:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.7rc202311220128 (2023-11-22) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6u5z format mmcif fromDatabase pdb 6u5z title: Cryo-EM structure of E. coli LonA S679A [more info...] Chain information for 6u5z #1 --- Chain | Description | UniProt A B C D E F | Lon protease | C3TLS2_ECOLX 1-784 > show atoms > hide atoms > show cartoons > open /home/azinas/Projects/Lon/Lon-LarA-max.pdb Chain information for Lon-LarA-max.pdb #2 --- Chain | Description A C D E F | No description available B | No description available L | No description available > show cartoons > hide atoms > color #1 #c64600ff > color #1 coral > color #1 #968cc7ff > color #2 #33d17aff > color #2 #efe09bff > select add #1 24606 atoms, 24972 bonds, 3174 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.96647,-0.25661,-0.0089855,39.479,-0.25521,-0.96388,0.076215,280.9,-0.028218,-0.071366,-0.99705,303.19 > view matrix models > #1,0.97582,0.021246,0.21754,-31.257,0.01102,-0.99878,0.048114,254.96,0.2183,-0.044553,-0.97487,264.37 > view matrix models > #1,0.9946,0.10002,0.027595,-16.487,0.10367,-0.96909,-0.22388,278.51,0.004349,0.22553,-0.97423,256.51 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.9946,0.10002,0.027595,68.494,0.10367,-0.96909,-0.22388,371.96,0.004349,0.22553,-0.97423,348.08 > view matrix models > #1,0.9946,0.10002,0.027595,71.289,0.10367,-0.96909,-0.22388,368.41,0.004349,0.22553,-0.97423,348.21 > view matrix models > #1,0.9946,0.10002,0.027595,76.695,0.10367,-0.96909,-0.22388,366.46,0.004349,0.22553,-0.97423,342.55 > ui tool show Matchmaker > matchmaker #1/A to #2/B pairing ss Parameters --- Chain pairing | ss 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 Lon-LarA-max.pdb, chain B (#2) with 6u5z, chain A (#1), sequence alignment score = 1822.3 RMSD between 213 pruned atom pairs is 1.244 angstroms; (across all 528 pairs: 4.285) > view matrix models > #1,0.50125,0.82487,-0.2614,90.711,0.84108,-0.53544,-0.076802,191.95,-0.20332,-0.18136,-0.96217,410.56 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.90597,0.27979,-0.3177,118.08,0.277,-0.9593,-0.054912,317.98,-0.32013,-0.038255,-0.9466,404.63 > view matrix models > #1,0.99328,-0.11464,-0.015647,114.82,-0.11154,-0.98467,0.13409,344.39,-0.03078,-0.13145,-0.99085,385.71 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.99328,-0.11464,-0.015647,112.86,-0.11154,-0.98467,0.13409,339.19,-0.03078,-0.13145,-0.99085,387.37 > view matrix models > #1,0.99328,-0.11464,-0.015647,112.24,-0.11154,-0.98467,0.13409,336.42,-0.03078,-0.13145,-0.99085,393.07 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > select subtract #1 Nothing selected Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > open /home/azinas/Projects/Lon/cryosparc_P7_J290_009_volume_map.mrc Summary of feedback from opening /home/azinas/Projects/Lon/cryosparc_P7_J290_009_volume_map.mrc --- notes | open kw {} Opened cryosparc_P7_J290_009_volume_map.mrc as #3, grid size 448,448,448, pixel 1.21, shown at level 0.0605, step 2, values float32 > select add #2 25829 atoms, 26224 bonds, 3339 residues, 1 model selected > select add #1 50435 atoms, 51196 bonds, 6513 residues, 2 models selected > view matrix models > #1,0.99328,-0.11464,-0.015647,199.14,-0.11154,-0.98467,0.13409,363.04,-0.03078,-0.13145,-0.99085,451.38,#2,1,0,0,86.893,0,1,0,26.614,0,0,1,58.311 > view matrix models > #1,0.99328,-0.11464,-0.015647,162.27,-0.11154,-0.98467,0.13409,379.71,-0.03078,-0.13145,-0.99085,443.63,#2,1,0,0,50.021,0,1,0,43.286,0,0,1,50.563 > view matrix models > #1,0.99328,-0.11464,-0.015647,166.51,-0.11154,-0.98467,0.13409,382.41,-0.03078,-0.13145,-0.99085,449.43,#2,1,0,0,54.268,0,1,0,45.988,0,0,1,56.361 > volume #3 step 1 > volume #3 level 0.1729 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.76347,-0.63559,-0.11459,280.8,-0.55624,-0.73728,0.38342,370.05,-0.32819,-0.22899,-0.91644,489.83,#2,0.833,0.52533,0.17359,-57.671,-0.47398,0.83944,-0.26587,245.35,-0.28539,0.13919,0.94825,102.31 > view matrix models > #1,0.78144,-0.55714,0.28097,208.91,-0.62022,-0.64419,0.4476,356.58,-0.068378,-0.52404,-0.84894,484.48,#2,0.83567,0.49912,-0.22922,37.297,-0.54921,0.76351,-0.33974,294.9,0.0054424,0.4098,0.91216,-12.536 > view matrix models > #1,0.75582,-0.57157,0.31945,208.36,-0.65476,-0.66344,0.36212,376.29,0.0049604,-0.48286,-0.87568,473.7,#2,0.81127,0.52134,-0.26466,45.932,-0.57997,0.77486,-0.25144,279.54,0.073986,0.35748,0.93098,-20.807 > select subtract #2 24606 atoms, 24972 bonds, 3174 residues, 1 model selected > select add #3 24606 atoms, 24972 bonds, 3174 residues, 3 models selected > fitmap #1 inMap #3 Fit molecule 6u5z (#1) to map cryosparc_P7_J290_009_volume_map.mrc (#3) using 24606 atoms average map value = 0.1823, steps = 192 shifted from previous position = 13 rotated from previous position = 20.3 degrees atoms outside contour = 13374, contour level = 0.17292 Position of 6u5z (#1) relative to cryosparc_P7_J290_009_volume_map.mrc (#3) coordinates: Matrix rotation and translation 0.89763698 -0.40231755 0.17996793 185.38287969 -0.43428791 -0.87699524 0.20560499 409.90031649 0.07511252 -0.26271652 -0.96194500 448.90386054 Axis -0.97368180 0.21800365 -0.06646920 Axis point 0.00000000 253.33101271 190.78415211 Rotation angle (degrees) 166.08453683 Shift along axis -120.98245329 > select subtract #1 2 models selected > select add #2 25829 atoms, 26224 bonds, 3339 residues, 3 models selected > fitmap #2 inMap #3 Fit molecule Lon-LarA-max.pdb (#2) to map cryosparc_P7_J290_009_volume_map.mrc (#3) using 25829 atoms average map value = 0.2185, steps = 116 shifted from previous position = 7.65 rotated from previous position = 4.68 degrees atoms outside contour = 10363, contour level = 0.17292 Position of Lon-LarA-max.pdb (#2) relative to cryosparc_P7_J290_009_volume_map.mrc (#3) coordinates: Matrix rotation and translation 0.78323429 0.57674751 -0.23217742 28.25439846 -0.61865551 0.76005404 -0.19895532 284.20952510 0.06172040 0.29946647 0.95210841 -14.27226863 Axis 0.37529584 -0.22129577 -0.90010067 Axis point 413.90900353 80.90830452 0.00000000 Rotation angle (degrees) 41.60860500 Shift along axis -39.44412873 > select subtract #2 2 models selected > select subtract #3 Nothing selected > hide #1 models > hide #!3 models > color #2 bychain > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for test_642d3_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #4 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_001.pdb Chain information for test_642d3_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_001.pdb #5 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_001.pdb Chain information for test_642d3_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_001.pdb #6 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb Chain information for test_642d3_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #7 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb Chain information for test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb #8 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for test_642d3_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_000.pdb #9 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_007_alphafold2_multimer_v3_model_2_seed_001.pdb Chain information for test_642d3_unrelaxed_rank_007_alphafold2_multimer_v3_model_2_seed_001.pdb #10 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_008_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for test_642d3_unrelaxed_rank_008_alphafold2_multimer_v3_model_3_seed_000.pdb #11 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_009_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for test_642d3_unrelaxed_rank_009_alphafold2_multimer_v3_model_1_seed_000.pdb #12 --- Chain | Description A | No description available B | No description available > open > /home/azinas/Downloads/a/test_642d3_unrelaxed_rank_010_alphafold2_multimer_v3_model_1_seed_001.pdb Chain information for test_642d3_unrelaxed_rank_010_alphafold2_multimer_v3_model_1_seed_001.pdb #13 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > matchmaker #4-13 to #2/A pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain A (#4), sequence alignment score = 2685.4 RMSD between 171 pruned atom pairs is 1.211 angstroms; (across all 542 pairs: 6.182) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_001.pdb, chain A (#5), sequence alignment score = 2685.4 RMSD between 172 pruned atom pairs is 1.205 angstroms; (across all 542 pairs: 5.291) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_001.pdb, chain A (#6), sequence alignment score = 2685.4 RMSD between 177 pruned atom pairs is 1.224 angstroms; (across all 542 pairs: 6.128) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb, chain A (#7), sequence alignment score = 2675.8 RMSD between 173 pruned atom pairs is 1.214 angstroms; (across all 542 pairs: 5.926) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb, chain A (#8), sequence alignment score = 2681.8 RMSD between 178 pruned atom pairs is 1.230 angstroms; (across all 542 pairs: 5.575) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_000.pdb, chain A (#9), sequence alignment score = 2681.8 RMSD between 164 pruned atom pairs is 1.192 angstroms; (across all 542 pairs: 5.181) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_007_alphafold2_multimer_v3_model_2_seed_001.pdb, chain A (#10), sequence alignment score = 2678.8 RMSD between 169 pruned atom pairs is 1.187 angstroms; (across all 542 pairs: 5.113) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_008_alphafold2_multimer_v3_model_3_seed_000.pdb, chain A (#11), sequence alignment score = 2678.2 RMSD between 169 pruned atom pairs is 1.198 angstroms; (across all 542 pairs: 5.354) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_009_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A (#12), sequence alignment score = 2679.4 RMSD between 172 pruned atom pairs is 1.206 angstroms; (across all 542 pairs: 4.919) Matchmaker Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_010_alphafold2_multimer_v3_model_1_seed_001.pdb, chain A (#13), sequence alignment score = 2682.4 RMSD between 173 pruned atom pairs is 1.188 angstroms; (across all 542 pairs: 4.792) > hide #2 models > show #2 models > matchmaker #4-13 to #2/B pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain A (#4), sequence alignment score = 2660.1 RMSD between 173 pruned atom pairs is 1.286 angstroms; (across all 540 pairs: 4.188) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_001.pdb, chain A (#5), sequence alignment score = 2660.1 RMSD between 216 pruned atom pairs is 1.385 angstroms; (across all 540 pairs: 3.371) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_001.pdb, chain A (#6), sequence alignment score = 2660.1 RMSD between 170 pruned atom pairs is 1.271 angstroms; (across all 540 pairs: 4.160) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb, chain A (#7), sequence alignment score = 2663.7 RMSD between 176 pruned atom pairs is 1.301 angstroms; (across all 540 pairs: 3.865) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb, chain A (#8), sequence alignment score = 2656.5 RMSD between 214 pruned atom pairs is 1.423 angstroms; (across all 540 pairs: 3.482) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_000.pdb, chain A (#9), sequence alignment score = 2656.5 RMSD between 216 pruned atom pairs is 1.387 angstroms; (across all 540 pairs: 3.411) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_007_alphafold2_multimer_v3_model_2_seed_001.pdb, chain A (#10), sequence alignment score = 2656.5 RMSD between 219 pruned atom pairs is 1.381 angstroms; (across all 540 pairs: 3.335) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_008_alphafold2_multimer_v3_model_3_seed_000.pdb, chain A (#11), sequence alignment score = 2652.9 RMSD between 212 pruned atom pairs is 1.393 angstroms; (across all 540 pairs: 3.445) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_009_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A (#12), sequence alignment score = 2667.3 RMSD between 219 pruned atom pairs is 1.341 angstroms; (across all 540 pairs: 3.142) Matchmaker Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_010_alphafold2_multimer_v3_model_1_seed_001.pdb, chain A (#13), sequence alignment score = 2660.1 RMSD between 237 pruned atom pairs is 1.365 angstroms; (across all 540 pairs: 3.210) > hide #13 models > show #13 models > hide #2 models > show #2 models > hide #2 models > matchmaker #4 to #2/A pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain A (#4), sequence alignment score = 2685.4 RMSD between 171 pruned atom pairs is 1.211 angstroms; (across all 542 pairs: 6.182) > matchmaker #5 to #2/B pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_001.pdb, chain A (#5), sequence alignment score = 2660.1 RMSD between 216 pruned atom pairs is 1.385 angstroms; (across all 540 pairs: 3.371) > matchmaker #6 to #2/C pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain C (#2) with test_642d3_unrelaxed_rank_003_alphafold2_multimer_v3_model_4_seed_001.pdb, chain A (#6), sequence alignment score = 2667.4 RMSD between 261 pruned atom pairs is 1.372 angstroms; (across all 542 pairs: 3.057) > matchmaker #7 to #2/D pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain D (#2) with test_642d3_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb, chain A (#7), sequence alignment score = 2685.4 RMSD between 306 pruned atom pairs is 1.260 angstroms; (across all 542 pairs: 2.534) > matchmaker #8 to #2/E pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain E (#2) with test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb, chain A (#8), sequence alignment score = 2483.2 RMSD between 228 pruned atom pairs is 1.318 angstroms; (across all 542 pairs: 3.669) > matchmaker #9 to #2/F pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain F (#2) with test_642d3_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_000.pdb, chain A (#9), sequence alignment score = 2679.1 RMSD between 303 pruned atom pairs is 1.335 angstroms; (across all 542 pairs: 2.596) > show #2 models > hide #2 models > show #2 models > hide #13 models > hide #12 models > hide #11 models > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > show #5 models > hide #4 models > hide #2 models > show #2 models > color #2 #f6f5f4ff > show #4 models > hide #5 models > show #5 models > hide #4 models > show #6 models > hide #5 models > color #6 #c061cbff > show #7 models > hide #6 models > show #8 models > hide #7 models > show #9 models > matchmaker #9 to #2/A pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain A (#2) with test_642d3_unrelaxed_rank_006_alphafold2_multimer_v3_model_2_seed_000.pdb, chain A (#9), sequence alignment score = 2681.8 RMSD between 164 pruned atom pairs is 1.192 angstroms; (across all 542 pairs: 5.181) > matchmaker #10 to #2/B pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_007_alphafold2_multimer_v3_model_2_seed_001.pdb, chain A (#10), sequence alignment score = 2656.5 RMSD between 219 pruned atom pairs is 1.381 angstroms; (across all 540 pairs: 3.335) > matchmaker #11 to #2/C pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain C (#2) with test_642d3_unrelaxed_rank_008_alphafold2_multimer_v3_model_3_seed_000.pdb, chain A (#11), sequence alignment score = 2673.4 RMSD between 287 pruned atom pairs is 1.319 angstroms; (across all 542 pairs: 2.821) > matchmaker #12 to #2/D pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain D (#2) with test_642d3_unrelaxed_rank_009_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A (#12), sequence alignment score = 2682.4 RMSD between 340 pruned atom pairs is 1.287 angstroms; (across all 542 pairs: 2.443) > matchmaker #13 to #2/E pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain E (#2) with test_642d3_unrelaxed_rank_010_alphafold2_multimer_v3_model_1_seed_001.pdb, chain A (#13), sequence alignment score = 2477.2 RMSD between 236 pruned atom pairs is 1.326 angstroms; (across all 542 pairs: 3.521) > hide #8 models > show #8 models > hide #9 models > show #9 models > hide #9 models > show #10 models > show #11 models > show #12 models > show #13 models > hide #12 models > hide #11 models > hide #10 models > matchmaker #8 to #2/D pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain D (#2) with test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb, chain A (#8), sequence alignment score = 2678.2 RMSD between 329 pruned atom pairs is 1.293 angstroms; (across all 542 pairs: 2.501) > matchmaker #8 to #2/B pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain B (#2) with test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb, chain A (#8), sequence alignment score = 2656.5 RMSD between 214 pruned atom pairs is 1.423 angstroms; (across all 540 pairs: 3.482) > matchmaker #8 to #2/F pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain F (#2) with test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb, chain A (#8), sequence alignment score = 2679.1 RMSD between 287 pruned atom pairs is 1.235 angstroms; (across all 542 pairs: 2.581) > matchmaker #8 to #2/E pairing bs Parameters --- Chain pairing | bs 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 Lon-LarA-max.pdb, chain E (#2) with test_642d3_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_001.pdb, chain A (#8), sequence alignment score = 2483.2 RMSD between 228 pruned atom pairs is 1.318 angstroms; (across all 542 pairs: 3.669) > hide #8 models > select add #13 6852 atoms, 6956 bonds, 888 residues, 1 model selected > color sel bychain An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 226, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings, transparent_drawings, camera) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 623, in _compute_shadowmaps shadow_enabled = r.shadow.use_shadow_map(camera, shadow_drawings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1482, in use_shadow_map shadow_map = self._finish_rendering_shadowmap() # Depth texture ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1512, in _finish_rendering_shadowmap fb = r.pop_framebuffer() ^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 764, in pop_framebuffer fb.activate() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 2313, in activate GL.glDrawBuffer(self._draw_buffer) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) ) OpenGL version: 3.3.0 NVIDIA 535.146.02 OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:0 Manufacturer: Micro-Star International Co., Ltd. Model: MS-7D67 OS: Ubuntu 23.10 Mantic Minotaur Architecture: 64bit ELF Virtual Machine: none CPU: 32 AMD Ryzen 9 7950X 16-Core Processor Cache Size: 1024 KB Memory: total used free shared buff/cache available Mem: 124Gi 24Gi 29Gi 438Mi 73Gi 100Gi Swap: 9Gi 3.5Mi 9Gi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD102 [GeForce RTX 4090] [10de:2684] (rev a1) Subsystem: NVIDIA Corporation AD102 [GeForce RTX 4090] [10de:16f3] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.13.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.12 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.2 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7rc202311220128 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 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-ISOLDE: 1.7rc1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MorphOT: 0.1 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NIHPresets: 1.1.17 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.1 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.45.0 funcparserlib: 2.0.0a0 glfw: 2.6.3 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.0 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 mrcfile: 1.5.0 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.0.0 progressbar2: 4.3.2 prompt-toolkit: 3.0.41 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 python-utils: 3.8.1 pytz: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Graphics can't reproduce all ChimeraX