id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18084 'DunbrackRotamerLibrary' object has no attribute 'display_name' jade.katinas@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description I am trying to mutate a threonine (Thr) to a phosphorylated threonine (TPO): Using Dunbrack library EBP1_rank_1.pdb #14/A THR 46: phi -164.3, psi 140.7 trans Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/cmd.py"", line 40, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py"", line 42, in swap_aa rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/swap_res/swap_res.py"", line 236, in get_rotamers params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/dunbrack_rotamer_lib/lib.py"", line 67, in rotamer_params return self._get_params(res_name, file_name, cache, archive) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB1763-4-15/Refine_20/FB1763-4-15_refine_020.pdb Chain information for FB1763-4-15_refine_020.pdb #1 --- Chain | Description A | No description available B | No description available > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB2623-1-39/Refine_28/FB2623-1-39_refine_028.pdb Chain information for FB2623-1-39_refine_028.pdb #2 --- Chain | Description A | No description available B | No description available > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB1763-4-15/Refine_20/FB1763-4-15_refine_020.pdb > format pdb Chain information for FB1763-4-15_refine_020.pdb #3 --- Chain | Description A | No description available B | No description available > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB1201-4-38/Refine_17/FB1201-4-38_refine_017.pdb Chain information for FB1201-4-38_refine_017.pdb #4 --- Chain | Description A | No description available B | No description available > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB7412-4-10/Refine_38/FB7412-4-10_refine_038.pdb Chain information for FB7412-4-10_refine_038.pdb #5 --- Chain | Description A | No description available B | No description available > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB3775-1-22/Refine_18/FB3775-1-22_refine_018.pdb Chain information for FB3775-1-22_refine_018.pdb #6 --- Chain | Description A | No description available > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec222024/Processed_data/FB6476-E3/Refine_21/FB6476-E3_refine_021.pdb Chain information for FB6476-E3_refine_021.pdb #7 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!2-7 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 FB1763-4-15_refine_020.pdb, chain B (#1) with FB2623-1-39_refine_028.pdb, chain B (#2), sequence alignment score = 1633.1 RMSD between 316 pruned atom pairs is 0.703 angstroms; (across all 335 pairs: 0.953) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB1763-4-15_refine_020.pdb, chain A (#3), sequence alignment score = 1733.2 RMSD between 336 pruned atom pairs is 0.000 angstroms; (across all 336 pairs: 0.000) Matchmaker FB1763-4-15_refine_020.pdb, chain B (#1) with FB1201-4-38_refine_017.pdb, chain A (#4), sequence alignment score = 1682.1 RMSD between 323 pruned atom pairs is 0.994 angstroms; (across all 334 pairs: 1.106) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB7412-4-10_refine_038.pdb, chain B (#5), sequence alignment score = 1667.5 RMSD between 312 pruned atom pairs is 0.552 angstroms; (across all 336 pairs: 1.171) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB3775-1-22_refine_018.pdb, chain A (#6), sequence alignment score = 1593.5 RMSD between 326 pruned atom pairs is 0.715 angstroms; (across all 335 pairs: 0.875) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB6476-E3_refine_021.pdb, chain A (#7), sequence alignment score = 1625.5 RMSD between 328 pruned atom pairs is 0.703 angstroms; (across all 336 pairs: 0.841) > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!5 models > show #!6 models > hide #!7 models > hide #!6 models > select #5/A 2392 atoms, 2433 bonds, 2 pseudobonds, 320 residues, 2 models selected > delete atoms (#!5 & sel) > delete bonds (#!5 & sel) > select #1/A 2552 atoms, 2597 bonds, 1 pseudobond, 337 residues, 2 models selected > select #1/B 2495 atoms, 2539 bonds, 1 pseudobond, 336 residues, 2 models selected > close #3 > close #5 > open > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB7412-4-10/Refine_38/FB7412-4-10_refine_038.pdb Chain information for FB7412-4-10_refine_038.pdb #3 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > matchmaker #!3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB7412-4-10_refine_038.pdb, chain B (#3), sequence alignment score = 1667.5 RMSD between 312 pruned atom pairs is 0.552 angstroms; (across all 336 pairs: 1.171) > select clear > select #3/A 2392 atoms, 2433 bonds, 2 pseudobonds, 320 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #1/B:233 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 56 atoms, 55 bonds, 8 residues, 1 model selected > select up 2113 atoms, 2151 bonds, 287 residues, 1 model selected > select up 2186 atoms, 2225 bonds, 297 residues, 1 model selected > select up 2481 atoms, 2524 bonds, 335 residues, 1 model selected > select up 2495 atoms, 2539 bonds, 336 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!2 models > hide #!3 models > select #2/B:201 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 65 atoms, 64 bonds, 8 residues, 1 model selected > select up 2079 atoms, 2117 bonds, 288 residues, 1 model selected > select up 2147 atoms, 2186 bonds, 298 residues, 1 model selected > select up 2421 atoms, 2464 bonds, 336 residues, 1 model selected > select up 2435 atoms, 2479 bonds, 337 residues, 1 model selected > delete atoms sel > delete bonds sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #1/C:10@O1 6 atoms, 4 bonds, 2 residues, 2 models selected > select up 10 atoms, 8 bonds, 2 residues, 2 models selected > select up 12 atoms, 9 bonds, 3 residues, 2 models selected > select up 15 atoms, 12 bonds, 3 residues, 2 models selected > delete atoms sel > delete bonds sel > select #1/C:3@O2 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #1/C:8@O4 6 atoms, 4 bonds, 2 residues, 1 model selected > select up 10 atoms, 8 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > hide #!2 models > show #!4 models > select #4/B:260 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 22 atoms, 22 bonds, 3 residues, 1 model selected > select up 2186 atoms, 2226 bonds, 288 residues, 1 model selected > select up 2350 atoms, 2393 bonds, 309 residues, 1 model selected > select up 2572 atoms, 2617 bonds, 336 residues, 1 model selected > select up 5220 atoms, 5297 bonds, 685 residues, 1 model selected > select down 2572 atoms, 2617 bonds, 336 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!6 models > hide #!4 models > show #!7 models > show #!4 models > show #!3 models > show #!2 models > ui tool show Matchmaker > matchmaker #!2-4,6-7 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 FB1763-4-15_refine_020.pdb, chain A (#1) with FB2623-1-39_refine_028.pdb, chain A (#2), sequence alignment score = 1512.5 RMSD between 312 pruned atom pairs is 0.622 angstroms; (across all 321 pairs: 3.470) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB7412-4-10_refine_038.pdb, chain B (#3), sequence alignment score = 1667.5 RMSD between 312 pruned atom pairs is 0.552 angstroms; (across all 336 pairs: 1.171) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB1201-4-38_refine_017.pdb, chain A (#4), sequence alignment score = 1675.7 RMSD between 314 pruned atom pairs is 0.867 angstroms; (across all 335 pairs: 1.144) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB3775-1-22_refine_018.pdb, chain A (#6), sequence alignment score = 1593.5 RMSD between 326 pruned atom pairs is 0.715 angstroms; (across all 335 pairs: 0.875) Matchmaker FB1763-4-15_refine_020.pdb, chain A (#1) with FB6476-E3_refine_021.pdb, chain A (#7), sequence alignment score = 1625.5 RMSD between 328 pruned atom pairs is 0.703 angstroms; (across all 336 pairs: 0.841) > select #3/C:2@O2 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > ui tool show ""Color Actions"" > set bgColor white > select ::name=""SO4"" 70 atoms, 56 bonds, 14 residues, 6 models selected > hide sel atoms > select ::name=""HOH"" 48 atoms, 48 residues, 6 models selected > hide sel atoms > select 15303 atoms, 15497 bonds, 8 pseudobonds, 2067 residues, 12 models selected > hide sel atoms > select clear > select ::name=""V12"" 15 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""V17"" 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""V26"" 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""V37"" 18 atoms, 19 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""V64"" 13 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""V74"" 15 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #7/A:83 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 4 residues, 1 model selected > select up 2164 atoms, 2201 bonds, 288 residues, 1 model selected > select up 2244 atoms, 2282 bonds, 298 residues, 1 model selected > select up 2548 atoms, 2590 bonds, 336 residues, 1 model selected > select up 2561 atoms, 2603 bonds, 337 residues, 1 model selected > select down 2548 atoms, 2590 bonds, 336 residues, 1 model selected > select up 2561 atoms, 2603 bonds, 337 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface ""FB6476-E3_refine_021.pdb_A SES surface"": minimum -28.6, mean -4.513, maximum 23.45 To also show corresponding color key, enter the above mlp command and add key true > select clear > select #1/A:44 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 76 atoms, 76 bonds, 12 residues, 1 model selected > select up 2164 atoms, 2203 bonds, 288 residues, 1 model selected > select up 2244 atoms, 2284 bonds, 298 residues, 1 model selected > select up 2538 atoms, 2582 bonds, 336 residues, 1 model selected > hide sel cartoons > select #2/A:43 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 2 residues, 1 model selected > select up 2029 atoms, 2067 bonds, 275 residues, 1 model selected > select up 2152 atoms, 2188 bonds, 294 residues, 1 model selected > select up 2360 atoms, 2398 bonds, 321 residues, 1 model selected > hide sel cartoons > select #3/B:244 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 54 atoms, 54 bonds, 7 residues, 1 model selected > select up 2203 atoms, 2242 bonds, 288 residues, 1 model selected > select up 2342 atoms, 2382 bonds, 309 residues, 1 model selected > select up 2564 atoms, 2606 bonds, 336 residues, 1 model selected > hide sel cartoons > select #7/A:87 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > hide surfaces > select #7/A:87 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 23 atoms, 22 bonds, 3 residues, 2 models selected > select up 2164 atoms, 2201 bonds, 288 residues, 2 models selected > select up 2244 atoms, 2282 bonds, 298 residues, 2 models selected > select up 2548 atoms, 2590 bonds, 336 residues, 2 models selected > hide sel cartoons > show sel surfaces > select clear > hide surfaces > select #4/A:86 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 44 atoms, 44 bonds, 6 residues, 1 model selected > select up 2211 atoms, 2250 bonds, 287 residues, 1 model selected > select up 2291 atoms, 2331 bonds, 297 residues, 1 model selected > select up 2604 atoms, 2648 bonds, 335 residues, 1 model selected > show sel surfaces > select clear > mlp Map values for surface ""FB3775-1-22_refine_018.pdb_A SES surface"": minimum -27.32, mean -3.845, maximum 21.48 Map values for surface ""FB1201-4-38_refine_017.pdb_A SES surface"": minimum -28.13, mean -4.243, maximum 22.28 Map values for surface ""FB2623-1-39_refine_028.pdb_A SES surface"": minimum -26.88, mean -4.383, maximum 23.05 Map values for surface ""FB1763-4-15_refine_020.pdb_A SES surface"": minimum -25.7, mean -3.937, maximum 21.78 Map values for surface ""FB6476-E3_refine_021.pdb_A SES surface"": minimum -28.6, mean -4.513, maximum 23.45 Map values for surface ""FB7412-4-10_refine_038.pdb_B SES surface"": minimum -26.12, mean -4.304, maximum 24.01 To also show corresponding color key, enter the above mlp command and add key true > select clear > hide surfaces > select #4/A:86 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 44 atoms, 44 bonds, 6 residues, 2 models selected > select up 2211 atoms, 2250 bonds, 287 residues, 2 models selected > select up 2291 atoms, 2331 bonds, 297 residues, 2 models selected > select up 2604 atoms, 2648 bonds, 335 residues, 2 models selected > show sel surfaces > select clear > save > /Users/katinaj/Documents/Vanderbilt/XrayData/Dec092024/jayproc/FB7412-4-10/Refine_38/FEM1BOverlay.cxs > close session > open ""/Users/katinaj/Downloads/7uhy (1).pdb"" format pdb 7uhy (1).pdb title: Human GATOR2 complex [more info...] Chain information for 7uhy (1).pdb #1 --- Chain | Description | UniProt A B | missing oocyte meiosis regulator homolog | MIO_HUMAN 1-875 C | WD repeat-containing protein 24 | WDR24_HUMAN 1-790 D | WD repeat-containing protein 59 | WDR59_HUMAN 1-974 E F G | isoform B of nucleoporin SEH1 | SEH1_HUMAN 1-421 H | protein SEC13 homolog | SEC13_HUMAN 1-322 I | unknown | J | unknown | Non-standard residues in 7uhy (1).pdb #1 --- ZN — zinc ion > close session > open ""/Users/katinaj/Downloads/7pe8 (1).pdb"" 7pe8 (1).pdb title: Cryo-em structure of deptor bound to human mtor complex 2, focussed on one protomer [more info...] Chain information for 7pe8 (1).pdb #1 --- Chain | Description | UniProt A | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-2549 C | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 E | rapamycin-insensitive companion of mtor | RICTR_HUMAN 1-1708 G | target of rapamycin complex 2 subunit MAPKAP1 | SIN1_HUMAN 1-522 I | DEP domain-containing protein 6 | DPTOR_HUMAN 1-409 Non-standard residues in 7pe8 (1).pdb #1 --- ACE — acetyl group IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) ZN — zinc ion > hide cartoons > show atoms > select 29291 atoms, 29830 bonds, 31 pseudobonds, 3835 residues, 3 models selected > hide sel atoms > show sel cartoons > select clear Drag select of 22 residues > close session > open /Users/katinaj/Downloads/4drh.pdb 4drh.pdb title: Co-crystal structure of the ppiase domain of FKBP51, rapamycin and the FRB fragment of mtor At low pH [more info...] Chain information for 4drh.pdb #1 --- Chain | Description | UniProt A D | peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 1-140 B E | serine/threonine-protein kinase mtor | MTOR_HUMAN 2025-2114 Non-standard residues in 4drh.pdb #1 --- RAP — rapamycin immunosuppressant drug SO4 — sulfate ion > select /D 1099 atoms, 1097 bonds, 157 residues, 1 model selected > delete atoms sel > delete bonds sel > select /E 758 atoms, 763 bonds, 1 pseudobond, 103 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select 1964 atoms, 1937 bonds, 299 residues, 1 model selected > hide sel atoms > select clear > select ::name=""RAP"" 65 atoms, 68 bonds, 1 residue, 1 model selected > show sel atoms > color sel lime > color sel byhetero > select clear > open > /Users/katinaj/Documents/Vanderbilt/Longevity/FRB/xraydata/FRBVU4592_xtalstructure/FRB4592_01_refine_8.pdb Chain information for FRB4592_01_refine_8.pdb #2 --- Chain | Description B | No description available > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 4drh.pdb, chain B (#1) with FRB4592_01_refine_8.pdb, chain B (#2), sequence alignment score = 480.5 RMSD between 88 pruned atom pairs is 0.783 angstroms; (across all 92 pairs: 2.086) > hide #!1 models > show #!1 models > hide #2 models > hide #!1 models > show #2 models > show #!1 models > hide #!1 models > select #2/B:2037 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 199 atoms, 206 bonds, 19 residues, 1 model selected > select up 947 atoms, 969 bonds, 92 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface ""FRB4592_01_refine_8.pdb_B SES surface"": minimum -24.26, mean -3.975, maximum 21.45 To also show corresponding color key, enter the above mlp command and add key true > select clear > transparency #2 70 > select clear > transparency #2 30 > select clear > close session > open > /Users/katinaj/Documents/Vanderbilt/Longevity/FRB/xraydata/FRBVU4592_xtalstructure/FRB4592_01_refine_8.pdb > format pdb Chain information for FRB4592_01_refine_8.pdb #1 --- Chain | Description B | No description available > open > /Users/katinaj/Documents/Vanderbilt/Longevity/FRB/xraydata/FRBVU4592_xtalstructure/FRB4592_01_refine_8.pdb > format pdb Chain information for FRB4592_01_refine_8.pdb #2 --- Chain | Description B | No description available > ui tool show ""Color Actions"" > set bgColor white > select #1/B:2031 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 199 atoms, 206 bonds, 19 residues, 1 model selected > select up 947 atoms, 969 bonds, 92 residues, 1 model selected > mlp sel Map values for surface ""FRB4592_01_refine_8.pdb_B SES surface"": minimum -24.87, mean -3.982, maximum 21.39 To also show corresponding color key, enter the above mlp command and add key true > select #1/A:2@NA 1 atom, 1 residue, 1 model selected > select up 3 atoms, 3 residues, 1 model selected > hide sel atoms > select #2/A:2@NA 1 atom, 1 residue, 1 model selected > select add #2/A:3@NA 2 atoms, 2 residues, 1 model selected > select add #2/A:1@NA 3 atoms, 3 residues, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 30 atoms, 32 bonds, 1 residue, 1 model selected > show sel surfaces > color sel byhetero Drag select of 2 residues > select up 298 atoms, 306 bonds, 28 residues, 3 models selected > select up 1894 atoms, 1938 bonds, 184 residues, 3 models selected > hide sel surfaces > show sel surfaces > transparency (#!1-2 & sel) 60 > select clear > select #1/B:2201@C10 1 atom, 1 residue, 1 model selected > select up 30 atoms, 32 bonds, 1 residue, 2 models selected > color (#!1 & sel) gray > color sel byhetero > select clear > select #1/B:2040@O 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 2 models selected > select up 199 atoms, 206 bonds, 19 residues, 2 models selected > select up 947 atoms, 969 bonds, 92 residues, 2 models selected > select down 199 atoms, 206 bonds, 19 residues, 2 models selected > select up 947 atoms, 969 bonds, 92 residues, 2 models selected > mlp sel Map values for surface ""FRB4592_01_refine_8.pdb_B SES surface"": minimum -24.87, mean -3.982, maximum 21.39 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > select #2/B:2033@O 1 atom, 1 residue, 1 model selected > select up 10 atoms, 9 bonds, 1 residue, 2 models selected > select up 199 atoms, 206 bonds, 19 residues, 2 models selected > select up 947 atoms, 969 bonds, 92 residues, 2 models selected > close #2 > select /B:2111 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 46 atoms, 46 bonds, 3 residues, 2 models selected > select up 947 atoms, 969 bonds, 92 residues, 2 models selected > show sel surfaces > select clear > select /B:2201@C10 1 atom, 1 residue, 1 model selected > select up 30 atoms, 32 bonds, 1 residue, 2 models selected > color sel byhetero > color sel bychain > color sel bypolymer > color sel bychain > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue VU9 (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/77/52vr4r5963q7wss_q3pgqvdm0000gp/T/tmp855l3krm/ante.in.mol2 -fi mol2 -o /var/folders/77/52vr4r5963q7wss_q3pgqvdm0000gp/T/tmp855l3krm/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (VU9) `` (VU9) `Welcome to antechamber 20.0: molecular input file processor.` (VU9) `` (VU9) `Info: Finished reading file (/var/folders/77/52vr4r5963q7wss_q3pgqvdm0000gp/T/tmp855l3krm/ante.in.mol2); atoms read (30), bonds read (32).` (VU9) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (VU9) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (VU9) `` (VU9) `` (VU9) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (VU9) `Info: Total number of electrons: 126; net charge: 0` (VU9) `` (VU9) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (VU9) `` (VU9) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (VU9) `` (VU9) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (VU9) `` Charges for residue VU9 determined Coulombic values for FRB4592_01_refine_8.pdb_B SES surface #1.2: minimum, -2.65, mean -0.07, maximum 3.08 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select /B:2201@C04 1 atom, 1 residue, 1 model selected > select up 30 atoms, 32 bonds, 1 residue, 2 models selected > color (#!1 & sel) dark gray > select /B:2110@NE 1 atom, 1 residue, 1 model selected > select up 17 atoms, 16 bonds, 1 residue, 2 models selected > select up 46 atoms, 46 bonds, 3 residues, 2 models selected > select up 947 atoms, 969 bonds, 92 residues, 2 models selected > hide sel surfaces > color (#!1 & sel) dim gray > color sel byhetero > select /B:2201@C11 1 atom, 1 residue, 1 model selected > select up 30 atoms, 32 bonds, 1 residue, 2 models selected > hide sel surfaces > color (#!1 & sel) cyan > select sel :< 5 146 atoms, 144 bonds, 14 residues, 1 model selected > show sel atoms > select clear [Repeated 1 time(s)] > select /A:2@NA 1 atom, 1 residue, 1 model selected > select add /A:3@NA 2 atoms, 2 residues, 1 model selected > hide sel atoms > select /B:2107 13 atoms, 13 bonds, 1 residue, 1 model selected > select up 149 atoms, 153 bonds, 14 residues, 2 models selected > select up 947 atoms, 969 bonds, 92 residues, 2 models selected > show sel surfaces > mlp sel Map values for surface ""FRB4592_01_refine_8.pdb_B SES surface"": minimum -24.87, mean -3.982, maximum 21.39 To also show corresponding color key, enter the above mlp command and add key true > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 30 atoms, 32 bonds, 1 residue, 2 models selected > color (#!1 & sel) magenta > select clear > transparency 60 > transparency 40 > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 30 atoms, 32 bonds, 1 residue, 2 models selected > show sel surfaces > transparency (#!1 & sel) 0 > select clear > select /B:2037@CB 1 atom, 1 residue, 1 model selected > select up 17 atoms, 16 bonds, 1 residue, 2 models selected > select up 199 atoms, 206 bonds, 19 residues, 2 models selected > select up 947 atoms, 969 bonds, 92 residues, 2 models selected > transparency (#!1 & sel) 50 > transparency (#!1 & sel) 30 > select clear [Repeated 1 time(s)] > close session > open /Users/katinaj/Downloads/7pea.pdb /Users/katinaj/Downloads/5wbj.pdb 7pea.pdb title: Cryo-em structure of deptor bound to human mtor complex 1, overall refinement [more info...] Chain information for 7pea.pdb #1 --- Chain | Description | UniProt A B | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-16 31-36 54-355 381-2549 C D | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 E F | regulatory-associated protein of mtor | RPTOR_HUMAN 1-1335 I J | DEP domain-containing protein 6 | DPTOR_HUMAN 1-409 Non-standard residues in 7pea.pdb #1 --- IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) 5wbj.pdb title: Crystal structure of the arabidopsis thaliana raptor In complex with the tos peptide of human 4EBP1 [more info...] Chain information for 5wbj.pdb #2 --- Chain | Description | UniProt A | regulatory-associated protein of tor 1 | RTOR1_ARATH 1-942 943-1344 T | eukaryotic translation initiation factor 4E-binding protein 1 | 4EBP1_HUMAN 99-118 > select 66631 atoms, 68063 bonds, 56 pseudobonds, 8402 residues, 4 models selected > hide sel atoms > show sel cartoons > select clear > open ""/Users/katinaj/Downloads/3fap (2).pdb"" 3fap (2).pdb title: Atomic structures of the rapamycin analogs In complex with both human FKBP12 and FRB domain of frap [more info...] Chain information for 3fap (2).pdb #3 --- Chain | Description | UniProt A | FKBP12 | FKB1A_HUMAN 1-107 B | FRAP | FRAP_HUMAN 108-201 Non-standard residues in 3fap (2).pdb #3 --- ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug) > ui tool show Matchmaker > matchmaker #3#!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7pea.pdb, chain A (#1) with 3fap (2).pdb, chain B (#3), sequence alignment score = 505 RMSD between 92 pruned atom pairs is 0.742 angstroms; (across all 94 pairs: 1.152) Matchmaker 7pea.pdb, chain E (#1) with 5wbj.pdb, chain A (#2), sequence alignment score = 2894.7 RMSD between 591 pruned atom pairs is 1.038 angstroms; (across all 1013 pairs: 3.563) > select #1/C:111 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 53 atoms, 54 bonds, 6 residues, 1 model selected > select up 2456 atoms, 2514 bonds, 317 residues, 1 model selected > hide sel cartoons > select #1/A:2183 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 63 atoms, 64 bonds, 7 residues, 1 model selected > select up 4623 atoms, 4724 bonds, 570 residues, 1 model selected > select down 63 atoms, 64 bonds, 7 residues, 1 model selected > select #1/I 795 atoms, 811 bonds, 106 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/J 795 atoms, 811 bonds, 106 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/T 68 atoms, 68 bonds, 8 residues, 1 model selected > select #1/E 8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected > select #1/F 8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/E 8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected > select #2/A 8311 atoms, 8503 bonds, 6 pseudobonds, 1058 residues, 2 models selected > select #1/A 17490 atoms, 17836 bonds, 20 pseudobonds, 2193 residues, 2 models selected > select #1/B 17490 atoms, 17836 bonds, 20 pseudobonds, 2193 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/D:287 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 39 atoms, 39 bonds, 5 residues, 1 model selected > select up 2456 atoms, 2514 bonds, 317 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/C 2456 atoms, 2514 bonds, 317 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show Matchmaker > matchmaker #2/A to #1/E 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 7pea.pdb, chain E (#1) with 5wbj.pdb, chain A (#2), sequence alignment score = 2894.7 RMSD between 591 pruned atom pairs is 1.038 angstroms; (across all 1013 pairs: 3.563) > select #2/T 68 atoms, 68 bonds, 8 residues, 1 model selected > color sel orange > select clear > ui tool show ""Color Actions"" > set bgColor white > hide #3 models > select add #1/A:2020 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 147 atoms, 146 bonds, 19 residues, 1 model selected > select add #1/A:2161 156 atoms, 154 bonds, 20 residues, 1 model selected > select up 170 atoms, 168 bonds, 22 residues, 1 model selected > select add #1/A:2131 178 atoms, 175 bonds, 23 residues, 1 model selected > select up 222 atoms, 220 bonds, 29 residues, 1 model selected > select add #1/A:2155 228 atoms, 225 bonds, 30 residues, 1 model selected > select up 253 atoms, 250 bonds, 33 residues, 1 model selected > select add #1/A:2174 261 atoms, 257 bonds, 34 residues, 1 model selected > select up 280 atoms, 276 bonds, 37 residues, 1 model selected > select add #1/A:2182 291 atoms, 287 bonds, 38 residues, 1 model selected > select up 343 atoms, 340 bonds, 44 residues, 1 model selected > select #1/A:2179 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 28 atoms, 28 bonds, 4 residues, 1 model selected > select add #1/A:2159 34 atoms, 33 bonds, 5 residues, 1 model selected > select up 51 atoms, 50 bonds, 7 residues, 1 model selected > select add #1/A:2155 57 atoms, 55 bonds, 8 residues, 1 model selected > select up 82 atoms, 80 bonds, 11 residues, 1 model selected > select add #1/A:2158 89 atoms, 87 bonds, 12 residues, 1 model selected > select up 94 atoms, 94 bonds, 13 residues, 1 model selected > select add #1/A:2174 102 atoms, 101 bonds, 14 residues, 1 model selected > select up 121 atoms, 121 bonds, 17 residues, 1 model selected > select add #1/A:2171 130 atoms, 129 bonds, 18 residues, 1 model selected > select up 213 atoms, 215 bonds, 28 residues, 1 model selected > select add #1/A:2184 224 atoms, 226 bonds, 29 residues, 1 model selected > select up 276 atoms, 280 bonds, 35 residues, 1 model selected > select add #1/A:2134 287 atoms, 290 bonds, 36 residues, 1 model selected > select up 428 atoms, 436 bonds, 54 residues, 1 model selected > select add #1/A:2189 438 atoms, 446 bonds, 55 residues, 1 model selected > select up 459 atoms, 468 bonds, 58 residues, 1 model selected > select add #1/A:2232 466 atoms, 474 bonds, 59 residues, 1 model selected > select up 494 atoms, 502 bonds, 63 residues, 1 model selected > select add #1/A:2237 502 atoms, 509 bonds, 64 residues, 1 model selected > select up 518 atoms, 526 bonds, 67 residues, 1 model selected > select add #1/A:1983 525 atoms, 532 bonds, 68 residues, 1 model selected > select up 531 atoms, 538 bonds, 69 residues, 1 model selected > select add #1/A:1987 542 atoms, 548 bonds, 70 residues, 1 model selected > select up 678 atoms, 687 bonds, 88 residues, 1 model selected > select add #1/A:1980 684 atoms, 692 bonds, 89 residues, 1 model selected > select up 755 atoms, 766 bonds, 98 residues, 1 model selected > hide sel cartoons > select #1/A:2090 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 158 atoms, 161 bonds, 18 residues, 1 model selected > select up 4623 atoms, 4724 bonds, 570 residues, 1 model selected > select down 158 atoms, 161 bonds, 18 residues, 1 model selected > select add #1/A:2071 166 atoms, 168 bonds, 19 residues, 1 model selected > select up 237 atoms, 241 bonds, 28 residues, 1 model selected > select add #1/A:2060 248 atoms, 251 bonds, 29 residues, 1 model selected > select up 268 atoms, 273 bonds, 32 residues, 1 model selected > select add #1/A:2056 273 atoms, 277 bonds, 33 residues, 1 model selected > select up 403 atoms, 411 bonds, 49 residues, 1 model selected > select add #1/A:2107 410 atoms, 417 bonds, 50 residues, 1 model selected > select up 608 atoms, 621 bonds, 72 residues, 1 model selected > select add #1/A:2026 616 atoms, 628 bonds, 73 residues, 1 model selected > select up 773 atoms, 793 bonds, 90 residues, 1 model selected > select add #1/A:2116 780 atoms, 800 bonds, 91 residues, 1 model selected > select up 797 atoms, 818 bonds, 93 residues, 1 model selected > select add #1/A:2119 804 atoms, 824 bonds, 94 residues, 1 model selected > select up 4623 atoms, 4724 bonds, 570 residues, 1 model selected > select down 804 atoms, 824 bonds, 94 residues, 1 model selected > select add #1/A:2131 812 atoms, 831 bonds, 95 residues, 1 model selected > select up 856 atoms, 877 bonds, 101 residues, 1 model selected > select add #1/A:2019 863 atoms, 883 bonds, 102 residues, 1 model selected > select up 1003 atoms, 1024 bonds, 120 residues, 1 model selected > color sel forest green > select #1/A:2124 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 36 atoms, 36 bonds, 4 residues, 1 model selected > color sel forest green > select #1/A:2120 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 23 atoms, 22 bonds, 3 residues, 1 model selected > color sel forest green > hide #!1 models > show #!1 models > hide #!2 models > open /Users/katinaj/Downloads/7pea.pdb 7pea.pdb title: Cryo-em structure of deptor bound to human mtor complex 1, overall refinement [more info...] Chain information for 7pea.pdb #4 --- Chain | Description | UniProt A B | serine/threonine-protein kinase mtor | MTOR_HUMAN 1-16 31-36 54-355 381-2549 C D | target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 E F | regulatory-associated protein of mtor | RPTOR_HUMAN 1-1335 I J | DEP domain-containing protein 6 | DPTOR_HUMAN 1-409 Non-standard residues in 7pea.pdb #4 --- IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol 1,2,3,4,5,6-hexakisphosphate) > hide sel atoms > select 94396 atoms, 96226 bonds, 81 pseudobonds, 12042 residues, 7 models selected > hide sel & #!1,4 atoms > show sel & #!1,4 cartoons > ui tool show Matchmaker > matchmaker #!4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7pea.pdb, chain A (#1) with 7pea.pdb, chain A (#4), sequence alignment score = 12654.3 RMSD between 2192 pruned atom pairs is 0.000 angstroms; (across all 2192 pairs: 0.000) > select clear > select #4/B:461 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 106 atoms, 107 bonds, 13 residues, 1 model selected > select up 453 atoms, 460 bonds, 57 residues, 1 model selected > select up 467 atoms, 473 bonds, 59 residues, 1 model selected > select up 708 atoms, 717 bonds, 90 residues, 1 model selected > select up 728 atoms, 736 bonds, 94 residues, 1 model selected > select up 833 atoms, 841 bonds, 115 residues, 1 model selected > select up 939 atoms, 951 bonds, 129 residues, 1 model selected > select up 17490 atoms, 17836 bonds, 2193 residues, 1 model selected > select up 58252 atoms, 59492 bonds, 7336 residues, 1 model selected > select down 17490 atoms, 17836 bonds, 2193 residues, 1 model selected > select down 939 atoms, 951 bonds, 129 residues, 1 model selected > select up 17490 atoms, 17836 bonds, 2193 residues, 1 model selected > select up 58252 atoms, 59492 bonds, 7336 residues, 1 model selected > select down 17490 atoms, 17836 bonds, 2193 residues, 1 model selected > ui tool show ""Color Actions"" > color sel olive drab target acs > select #1/A:64 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 130 atoms, 134 bonds, 14 residues, 1 model selected > select up 135 atoms, 139 bonds, 15 residues, 1 model selected > select up 17490 atoms, 17836 bonds, 2193 residues, 1 model selected > color sel olive drab target acs > select clear > select #1/A:1286 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 176 atoms, 179 bonds, 20 residues, 1 model selected > select add #1/A:1325 182 atoms, 184 bonds, 21 residues, 1 model selected > select up 280 atoms, 286 bonds, 33 residues, 1 model selected > select add #1/A:1264 288 atoms, 293 bonds, 34 residues, 1 model selected > select up 345 atoms, 352 bonds, 41 residues, 1 model selected > select add #1/A:1273 356 atoms, 362 bonds, 42 residues, 1 model selected > select up 384 atoms, 392 bonds, 46 residues, 1 model selected > color sel forest green target acs [Repeated 1 time(s)] > select add #1/A:1336 393 atoms, 400 bonds, 47 residues, 1 model selected > select up 520 atoms, 527 bonds, 63 residues, 1 model selected > select add #1/A:1330 528 atoms, 534 bonds, 64 residues, 1 model selected > select add #1/A:1386 539 atoms, 544 bonds, 65 residues, 1 model selected > select up 600 atoms, 607 bonds, 74 residues, 1 model selected > select add #1/A:1349 608 atoms, 614 bonds, 75 residues, 1 model selected > select up 617 atoms, 624 bonds, 76 residues, 1 model selected > select add #1/A:1352 626 atoms, 632 bonds, 77 residues, 1 model selected > select up 759 atoms, 768 bonds, 94 residues, 1 model selected > color sel forest green target acs > select add #1/A:1296 765 atoms, 773 bonds, 95 residues, 1 model selected > select up 4498 atoms, 4603 bonds, 554 residues, 1 model selected > color sel forest green target acs > select #1/A:1638 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 112 atoms, 113 bonds, 13 residues, 1 model selected > select add #1/A:1647 122 atoms, 123 bonds, 14 residues, 1 model selected > select up 144 atoms, 146 bonds, 17 residues, 1 model selected > select clear > select #1/A:2263 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 94 atoms, 94 bonds, 11 residues, 1 model selected > select add #1/A:2256 103 atoms, 102 bonds, 12 residues, 1 model selected > select up 202 atoms, 203 bonds, 23 residues, 1 model selected > select add #1/A:2305 210 atoms, 210 bonds, 24 residues, 1 model selected > select up 293 atoms, 295 bonds, 34 residues, 1 model selected > color sel forest green target acs > select #1/A:970 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 135 atoms, 138 bonds, 17 residues, 1 model selected > select add #1/A:955 143 atoms, 145 bonds, 18 residues, 1 model selected > select up 292 atoms, 299 bonds, 36 residues, 1 model selected > select add #1/A:961 300 atoms, 306 bonds, 37 residues, 1 model selected > select up 2339 atoms, 2391 bonds, 290 residues, 1 model selected > color sel magenta target acs > select clear > select #1/A:2113 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 205 atoms, 210 bonds, 23 residues, 1 model selected > select #1/A:2028 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 165 atoms, 172 bonds, 18 residues, 1 model selected > select add #1/A:2113 174 atoms, 180 bonds, 19 residues, 1 model selected > select up 370 atoms, 382 bonds, 41 residues, 1 model selected > select add #1/A:2077 378 atoms, 389 bonds, 42 residues, 1 model selected > select up 528 atoms, 543 bonds, 59 residues, 1 model selected > select add #1/A:2069 534 atoms, 548 bonds, 60 residues, 1 model selected > select up 607 atoms, 623 bonds, 69 residues, 1 model selected > select add #1/A:2051 615 atoms, 630 bonds, 70 residues, 1 model selected > select up 742 atoms, 760 bonds, 86 residues, 1 model selected > select add #1/A:2040 746 atoms, 763 bonds, 87 residues, 1 model selected > select up 766 atoms, 785 bonds, 89 residues, 1 model selected > color sel cornflower blue target acs > select #1/A:2117 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 24 atoms, 24 bonds, 3 residues, 1 model selected > color sel cornflower blue target acs > select #1/E:193 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 52 atoms, 53 bonds, 6 residues, 1 model selected > select up 1633 atoms, 1672 bonds, 202 residues, 1 model selected > color sel thistle target acs > color sel lavender target acs > select #1/E:324 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 176 atoms, 181 bonds, 22 residues, 1 model selected > select up 3568 atoms, 3656 bonds, 451 residues, 1 model selected > select up 3574 atoms, 3661 bonds, 452 residues, 1 model selected > select up 3849 atoms, 3944 bonds, 486 residues, 1 model selected > color sel lavender target acs > select #1/E:1096 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 54 atoms, 55 bonds, 6 residues, 1 model selected > select up 1375 atoms, 1411 bonds, 167 residues, 1 model selected > color sel lavender target acs > select #1/E:1237 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 45 atoms, 45 bonds, 5 residues, 1 model selected > select clear > select #4/B:1012 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 153 atoms, 155 bonds, 19 residues, 1 model selected > select up 2339 atoms, 2391 bonds, 290 residues, 1 model selected > color sel magenta target acs > select #4/B:1284 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 176 atoms, 179 bonds, 20 residues, 1 model selected > select up 4498 atoms, 4603 bonds, 554 residues, 1 model selected > color sel forest green target acs > select #4/B:2270 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 94 atoms, 94 bonds, 11 residues, 1 model selected > select up 4623 atoms, 4724 bonds, 570 residues, 1 model selected > select up 4646 atoms, 4745 bonds, 573 residues, 1 model selected > color sel pale green target acs > select up 9594 atoms, 9810 bonds, 1182 residues, 1 model selected > select down 4646 atoms, 4745 bonds, 573 residues, 1 model selected > color sel dark sea green target acs > select #1/A:1986 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 147 atoms, 148 bonds, 19 residues, 1 model selected > select up 4623 atoms, 4724 bonds, 570 residues, 1 model selected > color sel dark sea green target acs > select clear > select #1/A:2117 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 24 atoms, 24 bonds, 3 residues, 1 model selected > select up 4623 atoms, 4724 bonds, 570 residues, 1 model selected > select down 24 atoms, 24 bonds, 3 residues, 1 model selected > select add #1/A:2115 32 atoms, 31 bonds, 4 residues, 1 model selected > select up 229 atoms, 235 bonds, 26 residues, 1 model selected > select add #1/A:2074 241 atoms, 247 bonds, 27 residues, 1 model selected > select up 387 atoms, 396 bonds, 44 residues, 1 model selected > select add #1/A:2073 392 atoms, 400 bonds, 45 residues, 1 model selected > select up 466 atoms, 476 bonds, 54 residues, 1 model selected > select add #1/A:2024 476 atoms, 486 bonds, 55 residues, 1 model selected > select up 631 atoms, 648 bonds, 72 residues, 1 model selected > select add #1/A:2054 639 atoms, 655 bonds, 73 residues, 1 model selected > select up 766 atoms, 785 bonds, 89 residues, 1 model selected > select add #1/A:2040 770 atoms, 788 bonds, 90 residues, 1 model selected > select up 790 atoms, 810 bonds, 92 residues, 1 model selected > color sel cornflower blue target acs > select clear > color cornflower blue target acs > select #1/A:2061 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 31 atoms, 31 bonds, 4 residues, 1 model selected > color sel cornflower blue target acs > select clear > select #4/B:2095 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 205 atoms, 210 bonds, 23 residues, 1 model selected > select add #4/B:2051 213 atoms, 217 bonds, 24 residues, 1 model selected > select up 340 atoms, 347 bonds, 40 residues, 1 model selected > select add #4/B:2035 346 atoms, 352 bonds, 41 residues, 1 model selected > select up 505 atoms, 519 bonds, 58 residues, 1 model selected > select add #4/B:2041 514 atoms, 527 bonds, 59 residues, 1 model selected > select up 529 atoms, 544 bonds, 61 residues, 1 model selected > color sel cornflower blue target acs > select add #4/B:2077 537 atoms, 551 bonds, 62 residues, 1 model selected > select up 687 atoms, 705 bonds, 79 residues, 1 model selected > color sel cornflower blue target acs > select #4/B:2068 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 79 atoms, 79 bonds, 10 residues, 1 model selected > select add #4/B:2060 90 atoms, 89 bonds, 11 residues, 1 model selected > select up 110 atoms, 111 bonds, 14 residues, 1 model selected > select add #4/B:2118 118 atoms, 118 bonds, 15 residues, 1 model selected > select up 134 atoms, 135 bonds, 17 residues, 1 model selected > select add #4/B:2119 141 atoms, 141 bonds, 18 residues, 1 model selected > select add #4/B:2121 149 atoms, 148 bonds, 19 residues, 1 model selected > select up 164 atoms, 165 bonds, 21 residues, 1 model selected > color sel cornflower blue target acs > select clear > select #4/F:215 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 179 atoms, 180 bonds, 22 residues, 1 model selected > select up 1633 atoms, 1672 bonds, 202 residues, 1 model selected > color sel lavender target acs > select #4/F:473 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 70 atoms, 72 bonds, 8 residues, 1 model selected > select up 3568 atoms, 3656 bonds, 451 residues, 1 model selected > color sel lavender target acs > select #4/F:987 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 246 atoms, 248 bonds, 27 residues, 1 model selected > select up 1375 atoms, 1411 bonds, 167 residues, 1 model selected > select down 246 atoms, 248 bonds, 27 residues, 1 model selected > select up 1375 atoms, 1411 bonds, 167 residues, 1 model selected > select up 1384 atoms, 1419 bonds, 169 residues, 1 model selected > select down 1375 atoms, 1411 bonds, 167 residues, 1 model selected > select down 246 atoms, 248 bonds, 27 residues, 1 model selected > select add #4/F:965 257 atoms, 258 bonds, 28 residues, 1 model selected > select up 348 atoms, 354 bonds, 39 residues, 1 model selected > select add #4/F:953 353 atoms, 358 bonds, 40 residues, 1 model selected > select up 385 atoms, 391 bonds, 44 residues, 1 model selected > select add #4/F:839 397 atoms, 403 bonds, 45 residues, 1 model selected > select up 517 atoms, 525 bonds, 61 residues, 1 model selected > select add #4/F:955 524 atoms, 531 bonds, 62 residues, 1 model selected > select up 540 atoms, 549 bonds, 64 residues, 1 model selected > select add #4/F:971 547 atoms, 555 bonds, 65 residues, 1 model selected > select up 639 atoms, 652 bonds, 76 residues, 1 model selected > select add #4/F:816 647 atoms, 659 bonds, 77 residues, 1 model selected > select up 758 atoms, 774 bonds, 90 residues, 1 model selected > select add #4/F:821 766 atoms, 781 bonds, 91 residues, 1 model selected > select up 773 atoms, 791 bonds, 92 residues, 1 model selected > color sel lavender target acs > select clear > show #3 models > hide #!4 models > hide #!1 models > select #3/A:38 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 4 residues, 1 model selected > select up 832 atoms, 851 bonds, 107 residues, 1 model selected > select up 1006 atoms, 924 bonds, 213 residues, 1 model selected > select up 1890 atoms, 1742 bonds, 395 residues, 1 model selected > hide sel atoms > select clear > select #3/A 1006 atoms, 924 bonds, 213 residues, 1 model selected > color sel cornflower blue > color sel cyan > select #3/B:184 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 180 atoms, 185 bonds, 20 residues, 1 model selected > select up 796 atoms, 818 bonds, 94 residues, 1 model selected > ui tool show ""Color Actions"" > color sel violet target acs > select ::name=""ARD"" 69 atoms, 73 bonds, 1 residue, 1 model selected > show sel atoms > color sel orange > color sel byhetero > select clear > select #3/B:190 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 180 atoms, 185 bonds, 20 residues, 1 model selected > select up 796 atoms, 818 bonds, 94 residues, 1 model selected > show sel surfaces > select #3/A:52 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 46 atoms, 45 bonds, 6 residues, 1 model selected > select up 832 atoms, 851 bonds, 107 residues, 1 model selected > select up 1006 atoms, 924 bonds, 213 residues, 1 model selected > select down 832 atoms, 851 bonds, 107 residues, 1 model selected > hide sel cartoons > mlp sel Map values for surface ""3fap (2).pdb_A SES surface"": minimum -28.01, mean -4.647, maximum 24.6 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > select #3/B:194@CE2 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 2 models selected > select up 180 atoms, 185 bonds, 20 residues, 2 models selected > select up 796 atoms, 818 bonds, 94 residues, 2 models selected > select up 884 atoms, 818 bonds, 182 residues, 2 models selected > select down 796 atoms, 818 bonds, 94 residues, 2 models selected > mlp sel Map values for surface ""3fap (2).pdb_B SES surface"": minimum -27.62, mean -3.547, maximum 21.62 To also show corresponding color key, enter the above mlp command and add key true > select clear > transparency #3 60 > select clear > hide #!3 surfaces > select #3/A:402@C18 1 atom, 1 residue, 1 model selected > select up 69 atoms, 73 bonds, 1 residue, 1 model selected > select sel :< 5 644 atoms, 620 bonds, 78 residues, 3 models selected > show sel & #!3 atoms > select #3/A:54@N 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 46 atoms, 45 bonds, 6 residues, 2 models selected > select up 832 atoms, 851 bonds, 107 residues, 2 models selected > hide sel atoms > select #3/A:234@O 1 atom, 1 residue, 1 model selected > select up 1006 atoms, 924 bonds, 213 residues, 1 model selected > select down 1 atom, 1 residue, 2 models selected > select add #3/A:315@O 2 atoms, 2 residues, 1 model selected > select add #3/A:214@O 3 atoms, 3 residues, 1 model selected > select add #3/A:317@O 4 atoms, 4 residues, 1 model selected > select add #3/A:343@O 5 atoms, 5 residues, 1 model selected > select add #3/A:364@O 6 atoms, 6 residues, 1 model selected > select add #3/A:249@O 7 atoms, 7 residues, 1 model selected > select add #3/A:221@O 8 atoms, 8 residues, 1 model selected > select add #3/A:258@O 9 atoms, 9 residues, 1 model selected > hide sel atoms > select #3/B:194 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 180 atoms, 185 bonds, 20 residues, 2 models selected > select up 796 atoms, 818 bonds, 94 residues, 2 models selected > color sel byhetero > select clear > select #3/B:194 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 180 atoms, 185 bonds, 20 residues, 2 models selected > select up 796 atoms, 818 bonds, 94 residues, 2 models selected > select up 884 atoms, 818 bonds, 182 residues, 2 models selected > show sel surfaces > mlp sel Map values for surface ""3fap (2).pdb_B SES surface"": minimum -27.62, mean -3.547, maximum 21.62 To also show corresponding color key, enter the above mlp command and add key true > select clear > transparency #3 50 > select clear > select add #3/A:402@C20 1 atom, 5 bonds, 1 residue, 1 model selected > select add #3/A:402@C45 2 atoms, 11 bonds, 1 residue, 1 model selected > select add #3/A:402@O8 3 atoms, 11 bonds, 1 residue, 1 model selected > select add #3/A:402@O9 4 atoms, 12 bonds, 1 residue, 1 model selected > color sel lime > select add #3/A:402@C18 1 atom, 13 bonds, 1 residue, 1 model selected > color sel lime [Repeated 2 time(s)] > select clear > select #3/A:402@C43 1 atom, 1 residue, 1 model selected > color sel lime > select clear > select #3/A:402@C44 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C23 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C15 1 atom, 1 residue, 1 model selected > color sel lime > select #3/B:178@CB 1 atom, 1 residue, 1 model selected > select #3/B:178@CB 1 atom, 1 residue, 1 model selected > select #3/A:402@C26 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C25 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C24 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C50 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C22 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C21 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C19 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C17 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C16 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C49 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C54 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C53 1 atom, 1 residue, 1 model selected > color sel lime > select #3/A:402@C55 1 atom, 1 residue, 1 model selected > color sel lime > select clear [Repeated 1 time(s)] > select #3/A:402@C52 1 atom, 1 residue, 1 model selected > color sel lime > open ""/Users/katinaj/Downloads/4drh (1).pdb"" ""/Users/katinaj/Downloads/5gpg > (4).pdb"" 4drh (1).pdb title: Co-crystal structure of the ppiase domain of FKBP51, rapamycin and the FRB fragment of mtor At low pH [more info...] Chain information for 4drh (1).pdb #5 --- Chain | Description | UniProt A D | peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 1-140 B E | serine/threonine-protein kinase mtor | MTOR_HUMAN 2025-2114 Non-standard residues in 4drh (1).pdb #5 --- RAP — rapamycin immunosuppressant drug SO4 — sulfate ion 5gpg (4).pdb title: Co-crystal structure of the FK506 binding domain of human FKBP25, rapamycin and the FRB domain of human mtor [more info...] Chain information for 5gpg (4).pdb #6 --- Chain | Description | UniProt A | peptidyl-prolyl cis-trans isomerase FKBP3 | FKBP3_HUMAN 109-224 B | serine/threonine-protein kinase mtor | MTOR_HUMAN 2021-2112 Non-standard residues in 5gpg (4).pdb #6 --- RAP — rapamycin immunosuppressant drug > ui tool show Matchmaker > matchmaker #!5-6 to #3 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 3fap (2).pdb, chain B (#3) with 4drh (1).pdb, chain B (#5), sequence alignment score = 474.6 RMSD between 88 pruned atom pairs is 0.612 angstroms; (across all 93 pairs: 2.315) Matchmaker 3fap (2).pdb, chain B (#3) with 5gpg (4).pdb, chain B (#6), sequence alignment score = 510.9 RMSD between 84 pruned atom pairs is 0.556 angstroms; (across all 93 pairs: 1.149) > select #5/D 1099 atoms, 1097 bonds, 157 residues, 1 model selected > delete atoms sel > delete bonds sel > select #5/E 758 atoms, 763 bonds, 1 pseudobond, 103 residues, 2 models selected > delete atoms (#!5 & sel) > delete bonds (#!5 & sel) > select 98369 atoms, 99928 bonds, 82 pseudobonds, 12833 residues, 10 models selected > hide sel & #!3,5-6 atoms > hide sel & #!3,5-6 surfaces > select ::name=""ARD"" 69 atoms, 73 bonds, 1 residue, 1 model selected > show sel atoms > select #5/A:136 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 100 atoms, 102 bonds, 11 residues, 1 model selected > select up 1001 atoms, 1021 bonds, 132 residues, 1 model selected > select up 1136 atoms, 1117 bonds, 175 residues, 1 model selected > select up 1964 atoms, 1937 bonds, 299 residues, 1 model selected > select down 1136 atoms, 1117 bonds, 175 residues, 1 model selected > hide sel cartoons > select #6/A:221 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 82 atoms, 82 bonds, 10 residues, 1 model selected > select up 523 atoms, 534 bonds, 67 residues, 1 model selected > select up 548 atoms, 558 bonds, 70 residues, 1 model selected > select up 864 atoms, 883 bonds, 110 residues, 1 model selected > hide sel cartoons > select ::name=""RAP"" 130 atoms, 136 bonds, 2 residues, 2 models selected > show sel atoms > select clear > show #!1 models > hide #!1 models > show #!2 models > open ""/Users/katinaj/Downloads/5wbk (1).pdb"" 5wbk (1).pdb title: Crystal structure of the arabidopsis thaliana raptor In complex with the tos peptide of human S6K1 [more info...] Chain information for 5wbk (1).pdb #7 --- Chain | Description | UniProt A | regulatory-associated protein of tor 1 | RTOR1_ARATH 1-942 943-1344 T | ribosomal protein S6 kinase β-1 | KS6B1_HUMAN 1-14 > hide #!3 models > hide #!5 models > hide #!6 models > ui tool show Matchmaker > matchmaker #!7 to #2 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 5wbj.pdb, chain A (#2) with 5wbk (1).pdb, chain A (#7), sequence alignment score = 6225.2 RMSD between 1053 pruned atom pairs is 0.308 angstroms; (across all 1053 pairs: 0.308) > open ""/Users/katinaj/Downloads/4l46 (1).pdb"" 4l46 (1).pdb title: Crystal structures of human P70S6K1-WT [more info...] Chain information for 4l46 (1).pdb #8 --- Chain | Description | UniProt A | RPS6KB1 protein | Q7Z721_HUMAN 52-394 Non-standard residues in 4l46 (1).pdb #8 --- 5FI — 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole SO4 — sulfate ion ZN — zinc ion > hide #!2 models > open /Users/katinaj/Downloads/5wbh.pdb 5wbh.pdb title: Structure of the FRB domain of mtor bound to A substrate recruitment peptide of S6K1 [more info...] Chain information for 5wbh.pdb #9 --- Chain | Description | UniProt A B C D E | serine/threonine-protein kinase mtor | MTOR_HUMAN 2018-2114 W | ribosomal protein S6 kinase β-1 | KS6B1_HUMAN 389-414 > hide #!8 models > hide #!7 models > show #!2 models > show #!3 models > hide #!2 models > ui tool show Matchmaker > matchmaker #!3 to #9 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 5wbh.pdb, chain C (#9) with 3fap (2).pdb, chain B (#3), sequence alignment score = 514.6 RMSD between 92 pruned atom pairs is 0.555 angstroms; (across all 94 pairs: 0.825) > undo > hide #!3 models > hide #!2 models > show #!3 models > select 117659 atoms, 119245 bonds, 94 pseudobonds, 15034 residues, 16 models selected > hide sel & #9#!3 atoms > show sel & #9#!3 cartoons > select clear > select #9/C:2026 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 355 atoms, 362 bonds, 21 residues, 1 model selected > select up 1586 atoms, 1608 bonds, 96 residues, 1 model selected > select up 1637 atoms, 1608 bonds, 147 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/B:2076 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 472 atoms, 476 bonds, 29 residues, 1 model selected > select up 1532 atoms, 1554 bonds, 92 residues, 1 model selected > select up 1579 atoms, 1554 bonds, 139 residues, 1 model selected > select add #9/A:2076 1603 atoms, 1577 bonds, 140 residues, 1 model selected > select up 2051 atoms, 2030 bonds, 168 residues, 1 model selected > select up 3111 atoms, 3108 bonds, 231 residues, 1 model selected > select up 3179 atoms, 3108 bonds, 299 residues, 1 model selected > delete atoms sel > delete bonds sel > select #9/E:2075 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 472 atoms, 476 bonds, 29 residues, 1 model selected > select up 1560 atoms, 1582 bonds, 94 residues, 1 model selected > select up 1626 atoms, 1582 bonds, 160 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show Matchmaker > matchmaker #9 to #3 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 3fap (2).pdb, chain B (#3) with 5wbh.pdb, chain D (#9), sequence alignment score = 514 RMSD between 91 pruned atom pairs is 0.615 angstroms; (across all 91 pairs: 0.615) > show #!8 models > hide #!3 models > ui tool show Matchmaker > matchmaker #!8 to #9 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 5wbh.pdb, chain W (#9) with 4l46 (1).pdb, chain A (#8), sequence alignment score = 25.3 RMSD between 3 pruned atom pairs is 0.048 angstroms; (across all 3 pairs: 0.048) > ui tool show Matchmaker > matchmaker #8/A to #9/W 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 5wbh.pdb, chain W (#9) with 4l46 (1).pdb, chain A (#8), sequence alignment score = 25.3 RMSD between 3 pruned atom pairs is 0.048 angstroms; (across all 3 pairs: 0.048) > ui tool show ""Show Sequence Viewer"" > sequence chain #9/W Alignment identifier is 9/W > sequence chain #8/A Alignment identifier is 8/A > select #9/W:394-409 268 atoms, 270 bonds, 16 residues, 1 model selected > select > #8/A:68-76,80-87,96-103,135-141,144-150,155-156,201-203,209-211,390-391 409 atoms, 407 bonds, 49 residues, 1 model selected > select clear > show #!1 models > ui tool show Matchmaker > matchmaker #9#!2-8 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 7pea.pdb, chain A (#1) with 5wbh.pdb, chain D (#9), sequence alignment score = 511.3 RMSD between 92 pruned atom pairs is 0.699 angstroms; (across all 92 pairs: 0.699) Matchmaker 7pea.pdb, chain E (#1) with 5wbj.pdb, chain A (#2), sequence alignment score = 2894.7 RMSD between 591 pruned atom pairs is 1.038 angstroms; (across all 1013 pairs: 3.563) Matchmaker 7pea.pdb, chain A (#1) with 3fap (2).pdb, chain B (#3), sequence alignment score = 505 RMSD between 92 pruned atom pairs is 0.742 angstroms; (across all 94 pairs: 1.152) Matchmaker 7pea.pdb, chain A (#1) with 7pea.pdb, chain A (#4), sequence alignment score = 12654.3 RMSD between 2192 pruned atom pairs is 0.000 angstroms; (across all 2192 pairs: 0.000) Matchmaker 7pea.pdb, chain A (#1) with 4drh (1).pdb, chain B (#5), sequence alignment score = 478.5 RMSD between 88 pruned atom pairs is 0.747 angstroms; (across all 92 pairs: 2.026) Matchmaker 7pea.pdb, chain A (#1) with 5gpg (4).pdb, chain B (#6), sequence alignment score = 498.3 RMSD between 85 pruned atom pairs is 0.857 angstroms; (across all 93 pairs: 1.174) Matchmaker 7pea.pdb, chain E (#1) with 5wbk (1).pdb, chain A (#7), sequence alignment score = 2918.1 RMSD between 589 pruned atom pairs is 1.039 angstroms; (across all 1006 pairs: 3.430) Matchmaker 7pea.pdb, chain A (#1) with 4l46 (1).pdb, chain A (#8), sequence alignment score = 87.7 RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 232 pairs: 25.097) > hide #!8 models > hide #9 models > show #9 models > show #!7 models > hide #!7 models > show #!6 models > show #!8 models > hide #!8 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > hide #!3 models > open /Users/katinaj/Downloads/3ihy.pdb 3ihy.pdb title: Human PIK3C3 crystal structure [more info...] Chain information for 3ihy.pdb #10 --- Chain | Description | UniProt A B C D E | phosphatidylinositol 3-kinase catalytic subunit type 3 | PK3C3_HUMAN 282-879 > hide #!1 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!6 models > hide #9 models > select #10/A:471@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 34 atoms, 32 bonds, 4 residues, 1 model selected > select up 4343 atoms, 4428 bonds, 536 residues, 1 model selected > select up 21670 atoms, 22093 bonds, 2675 residues, 1 model selected > hide sel atoms > show sel cartoons > ui tool show Matchmaker > matchmaker #!10 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 7pea.pdb, chain A (#1) with 3ihy.pdb, chain B (#10), sequence alignment score = 555 RMSD between 153 pruned atom pairs is 1.221 angstroms; (across all 456 pairs: 21.078) > select #10/B 4340 atoms, 4423 bonds, 2 pseudobonds, 536 residues, 2 models selected > select #10/A 4343 atoms, 4428 bonds, 1 pseudobond, 536 residues, 2 models selected > delete atoms (#!10 & sel) > delete bonds (#!10 & sel) > select #10/C 4344 atoms, 4430 bonds, 1 pseudobond, 537 residues, 2 models selected > delete atoms (#!10 & sel) > delete bonds (#!10 & sel) > select #4/E 8385 atoms, 8585 bonds, 5 pseudobonds, 1052 residues, 2 models selected > select #10/D 4303 atoms, 4387 bonds, 1 pseudobond, 531 residues, 2 models selected > delete atoms (#!10 & sel) > delete bonds (#!10 & sel) > select #10/E 4340 atoms, 4425 bonds, 1 pseudobond, 535 residues, 2 models selected > delete atoms (#!10 & sel) > delete bonds (#!10 & sel) > ui tool show Matchmaker > matchmaker #!10 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 7pea.pdb, chain A (#1) with 3ihy.pdb, chain B (#10), sequence alignment score = 555 RMSD between 153 pruned atom pairs is 1.221 angstroms; (across all 456 pairs: 21.078) > hide #!4 models > select #10/B:829 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 44 atoms, 44 bonds, 6 residues, 1 model selected > select up 3220 atoms, 3281 bonds, 400 residues, 1 model selected > select up 3228 atoms, 3288 bonds, 401 residues, 1 model selected > select up 4331 atoms, 4416 bonds, 534 residues, 1 model selected > select clear > select ::name=""5FI"" 28 atoms, 31 bonds, 1 residue, 1 model selected > show #!10 atoms > hide #!10 atoms > show #!4 models > hide #!4 models > show #!4 models > hide #!10 models > show #!10 models > hide #!4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #10/B Alignment identifier is 10/B > select > #10/B:289-301,309-337,341-355,359-367,373-385,388-414,474-561,565-584,606-609,641-661,690-708,713-740,780-787,792-822,828-847,851-870 2991 atoms, 3023 bonds, 365 residues, 1 model selected > select clear > select > #10/B:289-301,309-337,341-355,359-367,373-385,388-414,474-561,565-584,606-609,641-661,690-708,713-740,780-787,792-822,828-847,851-870 2991 atoms, 3023 bonds, 365 residues, 1 model selected > select #10/B:328 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > select clear > select ::name=""5FI"" 28 atoms, 31 bonds, 1 residue, 1 model selected > show #!10 atoms > hide #!10 atoms > select #10/B:354 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 5 atom styles > color sel byhetero > color sel yellow > select #10/B:356 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > color sel yellow > color sel byhetero > select clear > show #!4 models > show #!1 models > hide #!4 models > select #1/A:1438 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 127 atoms, 130 bonds, 17 residues, 1 model selected > select up 4498 atoms, 4603 bonds, 554 residues, 1 model selected > select up 4534 atoms, 4638 bonds, 558 residues, 1 model selected > select up 11460 atoms, 11718 bonds, 1414 residues, 1 model selected > select down 4534 atoms, 4638 bonds, 558 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:869 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 107 atoms, 107 bonds, 13 residues, 1 model selected > select up 891 atoms, 905 bonds, 113 residues, 1 model selected > select up 906 atoms, 920 bonds, 115 residues, 1 model selected > select up 2008 atoms, 2039 bonds, 256 residues, 1 model selected > select up 2028 atoms, 2059 bonds, 259 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:316 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 111 atoms, 114 bonds, 15 residues, 1 model selected > select add #1/A:180 118 atoms, 121 bonds, 16 residues, 1 model selected > select up 165 atoms, 171 bonds, 21 residues, 1 model selected > select up 728 atoms, 742 bonds, 101 residues, 1 model selected > select up 734 atoms, 747 bonds, 102 residues, 1 model selected > select up 879 atoms, 895 bonds, 120 residues, 1 model selected > select up 886 atoms, 901 bonds, 121 residues, 1 model selected > select up 1332 atoms, 1355 bonds, 177 residues, 1 model selected > select up 1339 atoms, 1361 bonds, 178 residues, 1 model selected > select up 1436 atoms, 1459 bonds, 191 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:528 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 115 atoms, 116 bonds, 15 residues, 1 model selected > select up 409 atoms, 412 bonds, 53 residues, 1 model selected > select up 9492 atoms, 9677 bonds, 1185 residues, 1 model selected > select down 409 atoms, 412 bonds, 53 residues, 1 model selected > select add #1/A:624 420 atoms, 422 bonds, 54 residues, 1 model selected > select up 540 atoms, 543 bonds, 69 residues, 1 model selected > select add #1/A:607 545 atoms, 547 bonds, 70 residues, 1 model selected > select up 651 atoms, 657 bonds, 82 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear [Repeated 1 time(s)] > select #1/A:593 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 57 atoms, 54 bonds, 7 residues, 1 model selected > select add #1/A:588 64 atoms, 60 bonds, 8 residues, 1 model selected > select up 157 atoms, 155 bonds, 21 residues, 1 model selected > select add #1/A:578 162 atoms, 159 bonds, 22 residues, 1 model selected > select add #1/A:44 167 atoms, 163 bonds, 23 residues, 1 model selected > select up 242 atoms, 239 bonds, 38 residues, 1 model selected > select add #1/A:95 246 atoms, 242 bonds, 39 residues, 1 model selected > select up 350 atoms, 346 bonds, 54 residues, 1 model selected > select add #1/A:280 359 atoms, 354 bonds, 55 residues, 1 model selected > select up 468 atoms, 463 bonds, 68 residues, 1 model selected > select add #1/A:28 473 atoms, 467 bonds, 69 residues, 1 model selected > select up 533 atoms, 527 bonds, 81 residues, 1 model selected > select add #1/A:271 541 atoms, 534 bonds, 82 residues, 1 model selected > select up 649 atoms, 644 bonds, 96 residues, 1 model selected > select add #1/A:127 655 atoms, 649 bonds, 97 residues, 1 model selected > select up 757 atoms, 751 bonds, 111 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #1/A:115 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 133 atoms, 134 bonds, 16 residues, 1 model selected > select add #1/A:118 141 atoms, 141 bonds, 17 residues, 1 model selected > select up 193 atoms, 195 bonds, 25 residues, 1 model selected > select add #1/A:239 202 atoms, 203 bonds, 26 residues, 1 model selected > select up 308 atoms, 313 bonds, 38 residues, 1 model selected > select add #1/A:150 317 atoms, 321 bonds, 39 residues, 1 model selected > select up 459 atoms, 469 bonds, 55 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:64 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 130 atoms, 134 bonds, 14 residues, 1 model selected > select add #1/A:60 135 atoms, 138 bonds, 15 residues, 1 model selected > select add #1/A:259 143 atoms, 145 bonds, 1 pseudobond, 16 residues, 2 models selected > select up 199 atoms, 199 bonds, 1 pseudobond, 23 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/E:1182 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 32 atoms, 31 bonds, 5 residues, 1 model selected > select up 1296 atoms, 1316 bonds, 168 residues, 1 model selected > select up 1333 atoms, 1351 bonds, 174 residues, 1 model selected > select up 2903 atoms, 2969 bonds, 364 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/E:677 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 101 bonds, 12 residues, 1 model selected > select up 3568 atoms, 3656 bonds, 451 residues, 1 model selected > select up 3574 atoms, 3661 bonds, 452 residues, 1 model selected > select up 3849 atoms, 3944 bonds, 486 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/E:34 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 54 atoms, 54 bonds, 6 residues, 1 model selected > select up 1633 atoms, 1672 bonds, 202 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:2038 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 165 atoms, 172 bonds, 18 residues, 1 model selected > select up 4614 atoms, 4715 bonds, 569 residues, 1 model selected > select down 165 atoms, 172 bonds, 18 residues, 1 model selected > select add #1/A:2045 174 atoms, 180 bonds, 19 residues, 1 model selected > select up 300 atoms, 309 bonds, 35 residues, 1 model selected > select add #1/A:2067 309 atoms, 317 bonds, 36 residues, 1 model selected > select up 379 atoms, 388 bonds, 45 residues, 1 model selected > select add #1/A:2082 388 atoms, 396 bonds, 46 residues, 1 model selected > select up 537 atoms, 550 bonds, 63 residues, 1 model selected > select add #1/A:2097 545 atoms, 557 bonds, 64 residues, 1 model selected > select up 742 atoms, 760 bonds, 86 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:2061 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 59 atoms, 57 bonds, 8 residues, 1 model selected > select add #1/A:2116 66 atoms, 64 bonds, 9 residues, 1 model selected > select up 83 atoms, 81 bonds, 11 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/A:945 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 157 atoms, 161 bonds, 19 residues, 1 model selected > select up 2303 atoms, 2354 bonds, 286 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show Matchmaker > matchmaker #!10 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 7pea.pdb, chain A (#1) with 3ihy.pdb, chain B (#10), sequence alignment score = 451.2 RMSD between 153 pruned atom pairs is 1.221 angstroms; (across all 371 pairs: 12.792) > show #9 models > hide #9 models > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > show #9 models > open /Users/katinaj/Downloads/6bcx.cif Summary of feedback from opening /Users/katinaj/Downloads/6bcx.cif --- warnings | Atom HB3 is not in the residue template for UNK /A:17 Atom HB3 is not in the residue template for UNK /A:18 Atom HB3 is not in the residue template for UNK /A:19 Atom HB3 is not in the residue template for UNK /A:20 Atom HB3 is not in the residue template for UNK /A:21 4 messages similar to the above omitted Too many hydrogens missing from residue template(s) to warn about note | Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 6bcx.cif title: mTORC1 structure refined to 3.0 angstroms [more info...] Chain information for 6bcx.cif #11 --- Chain | Description | UniProt A B | Serine/threonine-protein kinase mTOR | MTOR_HUMAN 579-2549 D E | Target of rapamycin complex subunit LST8 | LST8_HUMAN 1-326 W Y | Regulatory-associated protein of mTOR | RPTOR_HUMAN 2-1335 X Z | Eukaryotic translation initiation factor 4E-binding protein 1 | 4EBP1_HUMAN 1-118 Non-standard residues in 6bcx.cif #11 --- ATP — adenosine-5'-triphosphate MG — magnesium ion > hide #9 models > hide #!10 models > hide #!11 models > hide #!1 models > show #!1 models > show #!4 models > hide #!1 models > show #!11 models > select 207590 atoms, 210143 bonds, 131 pseudobonds, 19366 residues, 21 models selected > hide sel & #!4,11 atoms > show sel & #!4,11 cartoons > ui tool show Matchmaker > matchmaker #!11 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7pea.pdb, chain A (#4) with 6bcx.cif, chain A (#11), sequence alignment score = 12420.3 RMSD between 2107 pruned atom pairs is 0.865 angstroms; (across all 2178 pairs: 0.969) > hide #!4 models > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > show sel atoms > color sel magenta > color sel byhetero > show #9 models > select clear > show #!2 models > hide #!2 models > show #!3 models > select clear > select ::name=""RAP"" 130 atoms, 136 bonds, 2 residues, 2 models selected > show #9#!3,11 atoms > hide #9#!3,11 atoms > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > show sel atoms > select ::name=""ARD"" 69 atoms, 73 bonds, 1 residue, 1 model selected > show sel atoms > select clear [Repeated 1 time(s)] > select #11/A:422 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 266 atoms, 267 bonds, 16 residues, 1 model selected > select up 938 atoms, 945 bonds, 57 residues, 1 model selected > select up 968 atoms, 974 bonds, 59 residues, 1 model selected > select up 1473 atoms, 1482 bonds, 90 residues, 1 model selected > select up 1513 atoms, 1521 bonds, 94 residues, 1 model selected > select up 1723 atoms, 1731 bonds, 115 residues, 1 model selected > select up 35079 atoms, 35421 bonds, 2181 residues, 1 model selected > select down 1723 atoms, 1731 bonds, 115 residues, 1 model selected > select #11/X 126 atoms, 126 bonds, 8 residues, 1 model selected > color sel lime > select #11/Z 126 atoms, 126 bonds, 8 residues, 1 model selected > color sel lime > select #11/W 16791 atoms, 16991 bonds, 5 pseudobonds, 1052 residues, 2 models selected > select clear > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > style sel sphere Changed 86 atom styles > select clear [Repeated 1 time(s)] > select #11/A:240 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 213 atoms, 216 bonds, 13 residues, 1 model selected > select up 237 atoms, 242 bonds, 14 residues, 1 model selected > select up 35079 atoms, 35421 bonds, 2181 residues, 1 model selected > select down 237 atoms, 242 bonds, 14 residues, 1 model selected > select up 35079 atoms, 35421 bonds, 2181 residues, 1 model selected > ui tool show ""Color Actions"" > color sel olive drab target acs > select #11/B:581 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 210 atoms, 210 bonds, 14 residues, 1 model selected > select up 264 atoms, 265 bonds, 18 residues, 1 model selected > select up 283 atoms, 283 bonds, 19 residues, 1 model selected > select up 833 atoms, 839 bonds, 53 residues, 1 model selected > select up 877 atoms, 882 bonds, 56 residues, 1 model selected > select up 3131 atoms, 3154 bonds, 196 residues, 1 model selected > select up 3145 atoms, 3167 bonds, 197 residues, 1 model selected > select up 4961 atoms, 4998 bonds, 309 residues, 1 model selected > select up 35079 atoms, 35421 bonds, 2181 residues, 1 model selected > color sel olive drab target acs > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > color sel magenta target acs [Repeated 1 time(s)] > color sel byhetero > select #11/A:2036 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 311 atoms, 318 bonds, 18 residues, 1 model selected > select add #11/A:2113 333 atoms, 339 bonds, 19 residues, 1 model selected > select up 722 atoms, 734 bonds, 41 residues, 1 model selected > select add #11/A:2116 736 atoms, 748 bonds, 42 residues, 1 model selected > select up 772 atoms, 785 bonds, 44 residues, 1 model selected > select add #11/A:2076 796 atoms, 808 bonds, 45 residues, 1 model selected > select up 1070 atoms, 1086 bonds, 61 residues, 1 model selected > select add #11/A:2054 1089 atoms, 1104 bonds, 62 residues, 1 model selected > select up 1341 atoms, 1359 bonds, 78 residues, 1 model selected > select add #11/A:2072 1358 atoms, 1375 bonds, 79 residues, 1 model selected > select up 1497 atoms, 1516 bonds, 88 residues, 1 model selected > color sel cornflower blue target acs > select #11/A:2092 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #11/A:2063 24 atoms, 22 bonds, 2 residues, 1 model selected > select up 80 atoms, 79 bonds, 6 residues, 1 model selected > color sel cornflower blue target acs > select clear > select #11/A:970 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 336 atoms, 340 bonds, 21 residues, 1 model selected > select up 4789 atoms, 4841 bonds, 290 residues, 1 model selected > color sel hot pink target acs > select #11/B:993 16 atoms, 15 bonds, 1 residue, 1 model selected > select up 270 atoms, 273 bonds, 16 residues, 1 model selected > select up 4789 atoms, 4841 bonds, 290 residues, 1 model selected > color sel hot pink target acs > hide #9 models > hide #!3 models > select clear > select #11/A:1308 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 101 atoms, 102 bonds, 7 residues, 1 model selected > select up 8931 atoms, 9036 bonds, 554 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale turquoise target acs > select #11/B:1297 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 90 atoms, 90 bonds, 6 residues, 1 model selected > select up 8931 atoms, 9036 bonds, 554 residues, 1 model selected > color sel pale turquoise target acs > select clear > turn 90 x Expected an axis vector or a keyword > turn x 90 [Repeated 3 time(s)] > turn x 45 > select clear > select #11/A:2040 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 46 atoms, 45 bonds, 3 residues, 1 model selected > color sel cornflower blue > select clear > show #9 models > select #11/A:3000@O2B 1 atom, 1 residue, 1 model selected > select up 43 atoms, 45 bonds, 1 residue, 1 model selected > style sel ball Changed 43 atom styles > select clear > show #!7 models > hide #!7 models > show #!3 models > select clear > hide #!3 models > hide #9 models > show #!3 models > select #3/A:61 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 80 atoms, 81 bonds, 10 residues, 2 models selected > select up 832 atoms, 851 bonds, 107 residues, 2 models selected > hide sel cartoons > select clear > select #3/A:402@O9 1 atom, 1 residue, 1 model selected > select add #11/A:3000@O3B 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #3/A:402@O9 #11/A:3000@O3B Distance between 3fap (2).pdb #3/A ARD 402 O9 and 6bcx.cif #11/A ATP 3000 O3B: 20.911Å > distance style color black [Repeated 2 time(s)] > select clear > ~distance #3/A:402@O9 #11/A:3000@O3B > select #11/A:2165 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 202 atoms, 202 bonds, 11 residues, 1 model selected > select up 9327 atoms, 9428 bonds, 570 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface ""6bcx.cif_A SES surface"": minimum -28.47, mean -3.145, maximum 27.31 To also show corresponding color key, enter the above mlp command and add key true > transparency (#!11 & sel) 80 > transparency (#!11 & sel) 60 > select clear > select #3/A:402@O8 1 atom, 1 residue, 1 model selected > select clear > hide #!3 models > show #!7 models > hide #!7 models > show #9 models > show #!8 models > hide #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > show #!3 models > hide #9 models > hide #!11 models > select #3/A 1006 atoms, 924 bonds, 213 residues, 1 model selected > show sel cartoons > select clear > open ""/Users/katinaj/Downloads/3fap (2).pdb"" 3fap (2).pdb title: Atomic structures of the rapamycin analogs In complex with both human FKBP12 and FRB domain of frap [more info...] Chain information for 3fap (2).pdb #12 --- Chain | Description | UniProt A | FKBP12 | FKB1A_HUMAN 1-107 B | FRAP | FRAP_HUMAN 108-201 Non-standard residues in 3fap (2).pdb #12 --- ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug) > hide #!3 models > show #!3 models > ui tool show Matchmaker > matchmaker #12 to #3 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 3fap (2).pdb, chain A (#3) with 3fap (2).pdb, chain A (#12), sequence alignment score = 559.6 RMSD between 107 pruned atom pairs is 0.000 angstroms; (across all 107 pairs: 0.000) > select clear > hide #!3 models > select #12/A:23 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 49 atoms, 50 bonds, 6 residues, 1 model selected > select up 832 atoms, 851 bonds, 107 residues, 1 model selected > select up 1006 atoms, 924 bonds, 213 residues, 1 model selected > select down 832 atoms, 851 bonds, 107 residues, 1 model selected > delete atoms sel > delete bonds sel > save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/ProteinDocking/FRB- > Rapamycin.pdb > open ""/Users/katinaj/Downloads/3fap (2).pdb"" 3fap (2).pdb title: Atomic structures of the rapamycin analogs In complex with both human FKBP12 and FRB domain of frap [more info...] Chain information for 3fap (2).pdb #13 --- Chain | Description | UniProt A | FKBP12 | FKB1A_HUMAN 1-107 B | FRAP | FRAP_HUMAN 108-201 Non-standard residues in 3fap (2).pdb #13 --- ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug) > hide #12 models > show #12 models > ui tool show Matchmaker > matchmaker #13 to #3 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 3fap (2).pdb, chain A (#3) with 3fap (2).pdb, chain A (#13), sequence alignment score = 559.6 RMSD between 107 pruned atom pairs is 0.000 angstroms; (across all 107 pairs: 0.000) > hide #12 models > select #13/A:101 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 93 atoms, 93 bonds, 11 residues, 1 model selected > select up 832 atoms, 851 bonds, 107 residues, 1 model selected > select up 1006 atoms, 924 bonds, 213 residues, 1 model selected > delete atoms sel > delete bonds sel > close #13 > open ""/Users/katinaj/Downloads/3fap (2).pdb"" 3fap (2).pdb title: Atomic structures of the rapamycin analogs In complex with both human FKBP12 and FRB domain of frap [more info...] Chain information for 3fap (2).pdb #13 --- Chain | Description | UniProt A | FKBP12 | FKB1A_HUMAN 1-107 B | FRAP | FRAP_HUMAN 108-201 Non-standard residues in 3fap (2).pdb #13 --- ARD — C15-(R)-methylthienyl rapamycin (rapamycin immunosuppressant drug) > ui tool show Matchmaker > matchmaker #13 to #3 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 3fap (2).pdb, chain A (#3) with 3fap (2).pdb, chain A (#13), sequence alignment score = 559.6 RMSD between 107 pruned atom pairs is 0.000 angstroms; (across all 107 pairs: 0.000) > select #13/A:102 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 93 atoms, 93 bonds, 11 residues, 1 model selected > select up 832 atoms, 851 bonds, 107 residues, 1 model selected > select up 1006 atoms, 924 bonds, 213 residues, 1 model selected > select down 832 atoms, 851 bonds, 107 residues, 1 model selected > delete atoms sel > delete bonds sel > select #13/B:199 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 180 atoms, 185 bonds, 20 residues, 1 model selected > select up 796 atoms, 818 bonds, 94 residues, 1 model selected > select down 180 atoms, 185 bonds, 20 residues, 1 model selected > delete atoms sel > delete bonds sel > select #13/B:166 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 241 atoms, 245 bonds, 29 residues, 1 model selected > select up 616 atoms, 632 bonds, 74 residues, 1 model selected > select up 704 atoms, 632 bonds, 162 residues, 1 model selected > select up 878 atoms, 705 bonds, 268 residues, 1 model selected > select up 209526 atoms, 211739 bonds, 19922 residues, 13 models selected > select down 878 atoms, 705 bonds, 268 residues, 4 models selected > select down 704 atoms, 632 bonds, 162 residues, 1 model selected > select up 878 atoms, 705 bonds, 268 residues, 1 model selected > select down 704 atoms, 632 bonds, 162 residues, 1 model selected > delete atoms sel > delete bonds sel > select ::name=""HOH"" 942 atoms, 942 residues, 7 models selected > delete atoms (#13 & sel) > delete bonds (#13 & sel) > save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Rapamycin.pdb > show #12 models > hide #13 models > save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/FRB-rap.pdb No model chosen to save relative to [Repeated 1 time(s)] > save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/FRB-Rap.cif models > #12 displayedOnly true Fetching CCD ARD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/ARD/ARD.cif > hide #12 models > show #13 models > save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Rap.cif models #13 > displayedOnly true > show #12 models > hide #13 models > save /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/FRB-Rap_Full.cif > models #12 > open /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Avogadro/Rapamycin- > EMin.pdb > /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/Avogadro/Rapamaycin_boundconformation.pdb Rapamaycin_boundconformation.pdb title: Rap [more info...] Non-standard residues in Rapamaycin_boundconformation.pdb #15 --- ARD — (ARD) > hide #12 models > show #14-15 atoms > select 208930 atoms, 211327 bonds, 131 pseudobonds, 19657 residues, 25 models selected > show sel & #14-15 atoms > ui tool show Matchmaker > matchmaker #14 to #15 No matrix compatible with both reference structure and all match structures > close #14-15 > show #!4 models > show #!3 models > show #9 models > open > /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/ProteinDocking/FRB-S6K1Dock.pdb FRB-S6K1Dock.pdb title: Human PIK3C3 crystal structure [more info...] Chain information for FRB-S6K1Dock.pdb #14 --- Chain | Description A | No description available D | No description available > ui tool show Matchmaker > matchmaker #!14 to #9 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 5wbh.pdb, chain D (#9) with FRB-S6K1Dock.pdb, chain D (#14), sequence alignment score = 513.9 RMSD between 92 pruned atom pairs is 0.157 angstroms; (across all 92 pairs: 0.157) > select clear > hide #!14 models > open > /Users/katinaj/Documents/Vanderbilt/Schrodinger/FRB/ProteinDocking/FRB-S6K1Dock2.pdb FRB-S6K1Dock2.pdb title: Human PIK3C3 crystal structure [more info...] Chain information for FRB-S6K1Dock2.pdb #15 --- Chain | Description A | No description available D | No description available > ui tool show Matchmaker > matchmaker #!15 to #9 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 5wbh.pdb, chain D (#9) with FRB-S6K1Dock2.pdb, chain D (#15), sequence alignment score = 513.9 RMSD between 92 pruned atom pairs is 0.157 angstroms; (across all 92 pairs: 0.157) > select #15/A 8757 atoms, 8842 bonds, 1 pseudobond, 536 residues, 2 models selected > select ::name=""THR"" 9831 atoms, 8871 bonds, 994 residues, 14 models selected > show sel & #9#!3-4,15 atoms > hide #!3 models > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > show #9#!4,15 atoms > hide #9#!4,15 atoms > select #15/A 8757 atoms, 8842 bonds, 1 pseudobond, 536 residues, 2 models selected > select clear > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > show #9#!4,15 atoms > hide #9#!4,15 atoms > show #!10 models > show #!11 models > hide #!10 models > select ::name=""THR"" 9831 atoms, 8871 bonds, 994 residues, 14 models selected > show sel & #9#!4,11,15 atoms > select clear > close #14-15 > show #!7 models > hide #!4 models > ui tool show Matchmaker > matchmaker #!7,11 to #4 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7pea.pdb, chain E (#4) with 5wbk (1).pdb, chain A (#7), sequence alignment score = 2918.1 RMSD between 589 pruned atom pairs is 1.039 angstroms; (across all 1006 pairs: 3.430) Matchmaker 7pea.pdb, chain A (#4) with 6bcx.cif, chain A (#11), sequence alignment score = 12420.3 RMSD between 2107 pruned atom pairs is 0.865 angstroms; (across all 2178 pairs: 0.969) > hide #9 models > ui tool show Matchmaker > matchmaker #!7 to #11 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 6bcx.cif, chain W (#11) with 5wbk (1).pdb, chain A (#7), sequence alignment score = 2885.7 RMSD between 599 pruned atom pairs is 1.051 angstroms; (across all 1002 pairs: 4.010) > select 208717 atoms, 211107 bonds, 131 pseudobonds, 19655 residues, 23 models selected > hide sel & #!7,11 atoms > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > show sel atoms > select clear > show #!3 models > select #11/W:104 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 293 atoms, 294 bonds, 19 residues, 1 model selected > select up 3272 atoms, 3311 bonds, 202 residues, 1 model selected > select up 3336 atoms, 3374 bonds, 206 residues, 1 model selected > select up 10473 atoms, 10600 bonds, 653 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface ""6bcx.cif_W SES surface"": minimum -28.2, mean -3.189, maximum 28.24 To also show corresponding color key, enter the above mlp command and add key true > select #3/A 1006 atoms, 924 bonds, 213 residues, 1 model selected > hide sel cartoons > hide sel atoms > select ::name=""RAP"" 130 atoms, 136 bonds, 2 residues, 2 models selected > show #!3,7,11 atoms > hide #!3,7,11 atoms > select #3/A 1006 atoms, 924 bonds, 213 residues, 1 model selected > show sel atoms > show sel cartoons > select #3/A:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 53 atoms, 52 bonds, 7 residues, 2 models selected > select up 832 atoms, 851 bonds, 107 residues, 2 models selected > hide sel atoms > hide sel cartoons > select #11/A:2359@CA 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 2 models selected > select up 101 atoms, 102 bonds, 7 residues, 2 models selected > select up 9327 atoms, 9428 bonds, 570 residues, 2 models selected > transparency (#!11 & sel) 30 > select #3/A:242@O 1 atom, 1 residue, 1 model selected > select ::name=""HOH"" 837 atoms, 837 residues, 6 models selected > hide sel & #!3 atoms > select ::name=""ATP"" 86 atoms, 90 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select #3/A:402@O8 1 atom, 1 residue, 1 model selected > select add #11/A:3000@O2B 2 atoms, 2 residues, 2 models selected > ui tool show Distances > distance #3/A:402@O8 #11/A:3000@O2B Distance between 3fap (2).pdb #3/A ARD 402 O8 and 6bcx.cif #11/A ATP 3000 O2B: 21.123Å > select clear > ~distance #3/A:402@O8 #11/A:3000@O2B > show #!10 models > hide #!10 models > show #9 models > hide #9#!3,7,11 surfaces > show #9#!3,7,11 surfaces > select #3/A:15@CB 1 atom, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 2 models selected > select up 92 atoms, 94 bonds, 12 residues, 2 models selected > hide sel surfaces > select #3/A:65@CG 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 80 atoms, 81 bonds, 10 residues, 2 models selected > select up 832 atoms, 851 bonds, 107 residues, 2 models selected > select up 1006 atoms, 924 bonds, 213 residues, 2 models selected > hide sel surfaces > hide #!7 models > hide #!3 models > select #9/D:2109@NH1 1 atom, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 1 residue, 2 models selected > select up 352 atoms, 357 bonds, 20 residues, 2 models selected > select up 1532 atoms, 1554 bonds, 92 residues, 2 models selected > select up 1619 atoms, 1554 bonds, 179 residues, 2 models selected > select up 1934 atoms, 1857 bonds, 213 residues, 2 models selected > mlp sel Map values for surface ""5wbh.pdb_D SES surface"": minimum -27.37, mean -3.145, maximum 23.9 Map values for surface ""5wbh.pdb_W SES surface"": minimum -20.12, mean -1.559, maximum 22.79 To also show corresponding color key, enter the above mlp command and add key true > select #9/W:401@CD 1 atom, 1 residue, 1 model selected > select up 15 atoms, 14 bonds, 1 residue, 2 models selected > select up 90 atoms, 90 bonds, 5 residues, 2 models selected > select up 300 atoms, 303 bonds, 19 residues, 2 models selected > transparency (#!9 & sel) 60 > show sel atoms > style sel stick Changed 300 atom styles > select clear > select #9/W:406@OE1 1 atom, 1 residue, 1 model selected > select up 15 atoms, 14 bonds, 1 residue, 2 models selected > select up 90 atoms, 91 bonds, 5 residues, 2 models selected > select up 300 atoms, 303 bonds, 19 residues, 2 models selected > color sel byhetero > mlp sel Map values for surface ""5wbh.pdb_W SES surface"": minimum -20.12, mean -1.559, maximum 22.79 To also show corresponding color key, enter the above mlp command and add key true > transparency (#!9 & sel) 80 > select clear > open /Users/katinaj/Downloads/EBP1_rank_1.pdb Chain information for EBP1_rank_1.pdb #14 --- Chain | Description A | No description available > hide #14 models > show #14 models > hide #!11 models > ui tool show Matchmaker > matchmaker #14 to #9/W 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 5wbh.pdb, chain W (#9) with EBP1_rank_1.pdb, chain A (#14), sequence alignment score = 19.4 RMSD between 10 pruned atom pairs is 1.508 angstroms; (across all 17 pairs: 4.785) > select #14/A:67 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 21 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > select #9/W:401@O 1 atom, 1 residue, 1 model selected > select up 15 atoms, 14 bonds, 1 residue, 2 models selected > select up 90 atoms, 90 bonds, 5 residues, 2 models selected > select up 300 atoms, 303 bonds, 19 residues, 2 models selected > hide sel surfaces > select #14/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 34 atoms, 33 bonds, 4 residues, 1 model selected > show sel atoms > select #14/A:65 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #14/A:62 6 atoms, 5 bonds, 1 residue, 1 model selected > select #14/A:61 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 34 atoms, 33 bonds, 4 residues, 1 model selected > select #14/A:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 47 atoms, 47 bonds, 5 residues, 1 model selected > show sel atoms > hide sel surfaces > select #9/D:2039@O 1 atom, 1 residue, 1 model selected > select up 20 atoms, 20 bonds, 1 residue, 2 models selected > select up 336 atoms, 343 bonds, 20 residues, 2 models selected > select up 1532 atoms, 1554 bonds, 92 residues, 2 models selected > select up 1619 atoms, 1554 bonds, 179 residues, 2 models selected > hide sel surfaces > style sel stick Changed 1619 atom styles > color sel byhetero > select clear > show #13 models > hide #13 models > show #12 models > hide #12 models > show #!11 models > hide #!9 models > hide #!11 models > select ::name=""THR"" 9103 atoms, 8191 bonds, 948 residues, 13 models selected > show sel & #14 atoms > show #!11 models > select #14/A:37 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 390 atoms, 398 bonds, 55 residues, 1 model selected > select down 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select #14/A:46 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 390 atoms, 398 bonds, 55 residues, 1 model selected > select down 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > show #!3 models > select #3/A 1006 atoms, 924 bonds, 213 residues, 1 model selected > show sel cartoons > select clear > hide #!11 models > select #14/A:112 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #14/A:113 15 atoms, 13 bonds, 2 residues, 1 model selected > select add #14/A:114 26 atoms, 24 bonds, 3 residues, 1 model selected > select add #14/A:115 35 atoms, 32 bonds, 4 residues, 1 model selected > select add #14/A:116 43 atoms, 39 bonds, 5 residues, 1 model selected > select add #14/A:118 51 atoms, 46 bonds, 6 residues, 1 model selected > select add #14/A:117 59 atoms, 53 bonds, 7 residues, 1 model selected > color sel purple > select clear > hide #!3 models > select #14/A:57 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel medium blue > ui tool show ""Color Actions"" > color sel light blue target acs > color sel byhetero > select #14/A:55 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel light blue target acs > color sel byhetero > select #14/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel light blue target acs > color sel byhetero target acs > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > select #14/A:70@CB 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > ui tool show AlphaFold > alphafold search #14 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json Webservices job id: INTDN15CQKO6V8UL BlastProtein failed: failed BlastProtein failed: 'bytes' object has no attribute 'items' Parsing BlastProtein results failed: 'NoneType' object has no attribute 'keys' > alphafold predict #14 minimize true AlphaFold Service Broken ## AlphaFold Prediction Requires Newer ChimeraX Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later. The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024. > ui tool show ""Modeller Comparative"" Populating font family aliases took 69 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > toolshed show > swapaa /14:A:46 TPO No amino acid residues specified for swapping > swapaa #14/A:46 TPO Using Dunbrack library EBP1_rank_1.pdb #14/A THR 46: phi -164.3, psi 140.7 trans Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/swap_res/cmd.py"", line 40, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 42, in swap_aa rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 236, in get_rotamers params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/dunbrack_rotamer_lib/lib.py"", line 67, in rotamer_params return self._get_params(res_name, file_name, cache, archive) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) See log for complete Python traceback. > swapaa #14/A:46 TPO Using Dunbrack library EBP1_rank_1.pdb #14/A THR 46: phi -164.3, psi 140.7 trans Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/swap_res/cmd.py"", line 40, in swap_aa swap_res.swap_aa(session, residues, res_type, bfactor=bfactor, clash_hbond_allowance=hbond_allowance, File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 42, in swap_aa rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/swap_res/swap_res.py"", line 236, in get_rotamers params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/dunbrack_rotamer_lib/lib.py"", line 67, in rotamer_params return self._get_params(res_name, file_name, cache, archive) File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' AttributeError: 'DunbrackRotamerLibrary' object has no attribute 'display_name' File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/rotamers/rot_lib.py"", line 186, in _get_params ""%s library does not support residue type '%s'"" % (self.display_name, base_name)) See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac21,1 Model Number: Z12Q000VBLL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 39 days, 23 hours, 1 minute Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 4.5K (4480 x 2520) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Structure Editing duplicate all ChimeraX