id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20533 Find Cavities not disposing of deleted structures mdooley302@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.7.3-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description I am trying to save a session file after running kvfinder. Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs Log from Wed Jun 24 12:28:31 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs > format session Log from Wed Jun 24 12:20:33 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/morgandooley/Documents/GltPh_Oligomerization/cavity_figure_base.cxs > format session Log from Mon Jun 22 18:10:19 2026UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/morgandooley/Documents/GltPh_Oligomerization/gltph_wCavity.cif Summary of feedback from opening /Users/morgandooley/Documents/GltPh_Oligomerization/gltph_wCavity.cif --- warnings | Unknown polymer entity '1' on line 36 Missing or incorrect sequence information. Inferred polymer connectivity. Missing entity information. Treating each chain as a separate entity. Atom XP is not in the residue template for CAV /X:6 Chain information for gltph_wCavity.cif --- Chain | Description 1.1/A 1.1/B 1.1/C | No description available Computing secondary structure > select protein & cavity :< 4.5 Expected a keyword > select #2:CAV :< 4.5 Nothing selected > select #1:CAV :< 4.5 1501 atoms, 234 bonds, 31 residues, 2 models selected > name contacts sel > name list contacts sel > name delete contacts sel Expected fewer arguments > name delete contacts > name list There are no user-defined specifier names. > name contacts_cav sel > name list contacts_cav sel > ~select #2:CAV 1501 atoms, 234 bonds, 31 residues, 2 models selected > ~select #1:CAV 249 atoms, 234 bonds, 30 residues, 1 model selected > name contacts_only sel > select clear > select contacts_only Nothing selected > name delete Missing or invalid ""name"" argument: Expected a text string > name delete contacts_only > name delete contacts_cav > select #1:CAV :< 4.5 ~sel #1:CAV Expected a keyword > select #1:CAV :< 4.5 1501 atoms, 234 bonds, 31 residues, 2 models selected > ~select #1:CAV 249 atoms, 234 bonds, 30 residues, 1 model selected > namesel contacts_only sel Unknown command: namesel contacts_only sel > name frozen contacts_only sel > select clear > select contacts_only 249 atoms, 234 bonds, 30 residues, 1 model selected > select #1 10738 atoms, 9666 bonds, 1249 residues, 3 models selected > ~select ~contacts_only 249 atoms, 234 bonds, 30 residues, 1 model selected > select #1 10738 atoms, 9666 bonds, 1249 residues, 3 models selected > ~select ~contacts_only 249 atoms, 234 bonds, 30 residues, 1 model selected > color contacts_only red > color all gray 80 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1 gray 80 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1:all gray 80 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1 all gray 80 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color all gray 80 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select #1:CAV 1252 atoms, 1 residue, 1 model selected > surface #1:CAV > name cavity surface #1:CAV ""surface #1:CAV"": invalid atom specifier > name cavity #1:CAV > select clear > surface cavity > select cavity 1252 atoms, 1 residue, 1 model selected > transparency cavity 50 > name list cavity #1:CAV contacts_only [249 atoms, 468 bonds] > show contacts_only atoms > style contacts_only stick Changed 249 atom styles > color concacts_only bypolymer Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color concacts_only byatom Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color concacts_only bymodel Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color contacts_only bymodel > color contacts_only byatom > color contacts_only bymodel > color contacts_only byatom > label contacts_only residues > hide #1 atoms > show #1 cartoons > color #1 gray80 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1 gray 80 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > hide #!1.2 models > show #!1.2 models > hide #!1.1 models > show #!1.1 models > color #1 gray > transparency #1 cartoons 30 Missing or invalid ""percent"" argument: Expected a number > transparency #1 30 > show contacts_only atoms > color contacts_only red > color contacts_only byatom > select ~contacts_only 10489 atoms, 9384 bonds, 1219 residues, 4 models selected > select #1:CAV :< 4.5 1501 atoms, 234 bonds, 31 residues, 2 models selected > ~select #1:CAV :< 4.5 1 model selected > select #1:CAV :< 4.5 1501 atoms, 234 bonds, 31 residues, 2 models selected > name cav_n_contacts #1:CAV :< 4.5 > ~select cav_n_contacts 1 model selected > transparency #1 70 cartoons > transparency contacts_only 0 cartoons > transparency contacts_only 0 atoms > select cavity 1252 atoms, 1 residue, 1 model selected > color cavity green > color cavity blue > transparency cavity 80 > select contacts_only :> 15 6417 atoms, 6528 bonds, 846 residues, 1 model selected > transparency sel 40 All > transparency sel 90 All > transparency sel 100 All > select contacts_only :> 10 7400 atoms, 7520 bonds, 985 residues, 1 model selected > select contacts_only :> 10, ~sel contacts_only :> 15 Expected a keyword > select contacts_only :> 10, ~sel contacts_only :> 15 Expected a keyword > select contacts_only :> 10 7400 atoms, 7520 bonds, 985 residues, 1 model selected > ~select contacts_only :> 15 983 atoms, 944 bonds, 139 residues, 1 model selected > transparency sel 80 All > select clear > set bgColor white > lighting soft > lighting full > lighting simple > set bgColor black > save > /Users/morgandooley/Documents/GltPh_Oligomerization/cavity_figure_base.cxs ——— End of log from Mon Jun 22 18:10:19 2026 ——— > view name session-start opened ChimeraX session > close session > open 6X15 format mmcif fromDatabase pdb 6x15 title: Inward-facing state of the glutamate transporter homologue GltPh in complex with L-aspartate and sodium ions [more info...] Chain information for 6x15 #1 --- Chain | Description A B C | Glutamate transporter homologue GltPh Non-standard residues in 6x15 #1 --- 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate ASP — aspartic acid HG — mercury (II) ion NA — sodium ion > save > /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs ——— End of log from Wed Jun 24 12:20:33 2026 ——— > view name session-start opened ChimeraX session > select add #1.1 51 pseudobonds, 1 model selected > hide sel > select subtract #1.1 Nothing selected > select add #1 10026 atoms, 10146 bonds, 51 pseudobonds, 1320 residues, 2 models selected > select subtract #1 Nothing selected > select /a-c 10026 atoms, 10146 bonds, 51 pseudobonds, 1320 residues, 2 models selected > select :6OU,NA,HG 654 atoms, 603 bonds, 51 residues, 1 model selected > hide sel > select /a-c 10026 atoms, 10146 bonds, 51 pseudobonds, 1320 residues, 2 models selected > hide atoms > select :1-75,120-220 4065 atoms, 4161 bonds, 528 residues, 1 model selected > select :1-70,120-220 3969 atoms, 4062 bonds, 513 residues, 1 model selected > select :1-70,125-220 3834 atoms, 3921 bonds, 498 residues, 1 model selected > select :1-75,125-220 3930 atoms, 4020 bonds, 513 residues, 1 model selected > name frozen scaffold sel > select ~sel & ##selected 6096 atoms, 6126 bonds, 51 pseudobonds, 807 residues, 2 models selected > name frozen transport sel > save > /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs > color (#!1 & sel) light gray > select ~sel & ##selected 3930 atoms, 4020 bonds, 513 residues, 1 model selected > color sel cornflower blue > select clear > save > /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs ——— End of log from Wed Jun 24 12:28:31 2026 ——— > view name session-start opened ChimeraX session > name list scaffold [3930 atoms, 4020 bonds] transport [6096 atoms, 6126 bonds, 2 models] > ui tool show ""Find Cavities"" > kvfinder gridSpacing 0.7 probeIn 1.2 probeOut 5.5 99 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.45 | | 1335.99 | 899.35 | 3895 | 0 | 0 1.2.33 | | 1001.9 | 883.06 | 2921 | 6.96 | 1.54 1.2.58 | | 995.39 | 854.89 | 2902 | 7.03 | 1.52 1.2.8 | | 945.99 | 827.7 | 2758 | 6.93 | 1.55 1.2.27 | | 747.05 | 573.24 | 2178 | 8.1 | 2.09 1.2.70 | | 664.05 | 455.94 | 1936 | 9.8 | 2.13 1.2.44 | | 648.27 | 450.94 | 1890 | 9.1 | 2.3 1.2.79 | | 133.77 | 109.63 | 390 | 2.89 | 0.78 1.2.20 | | 127.25 | 117.26 | 371 | 2.21 | 0.6 1.2.49 | | 126.91 | 127.16 | 370 | 2.32 | 0.73 1.2.7 | | 120.05 | 152.62 | 350 | 0 | 0 1.2.85 | | 117.31 | 124.38 | 342 | 6.93 | 3.75 1.2.61 | | 116.62 | 124.05 | 340 | 0 | 0 1.2.16 | | 115.25 | 124.32 | 336 | 0 | 0 1.2.72 | | 114.22 | 144.44 | 333 | 0 | 0 1.2.78 | | 113.88 | 140.31 | 332 | 0 | 0 1.2.55 | | 104.96 | 95.02 | 306 | 2.1 | 0.46 1.2.89 | | 85.41 | 123.8 | 249 | 0 | 0 1.2.17 | | 85.06 | 132.43 | 248 | 0 | 0 1.2.53 | | 77.52 | 118.11 | 226 | 0 | 0 1.2.83 | | 77.52 | 122.53 | 226 | 6.06 | 2.34 1.2.38 | | 65.51 | 83.36 | 191 | 2.1 | 0.8 1.2.93 | | 64.14 | 69.56 | 187 | 2.89 | 0.9 1.2.12 | | 62.77 | 64.07 | 183 | 2.89 | 0.97 1.2.47 | | 56.25 | 60.53 | 164 | 2.62 | 0.93 1.2.77 | | 37.04 | 57.78 | 108 | 0 | 0 1.2.43 | | 34.3 | 59.26 | 100 | 0 | 0 1.2.80 | | 34.3 | 55.77 | 100 | 4.48 | 1.55 1.2.60 | | 33.96 | 59.15 | 99 | 0 | 0 1.2.41 | | 32.58 | 53.45 | 95 | 0 | 0 1.2.84 | | 31.9 | 49.67 | 93 | 3.77 | 1.33 1.2.29 | | 31.21 | 52.45 | 91 | 0 | 0 1.2.30 | | 30.53 | 47.8 | 89 | 0 | 0 1.2.69 | | 30.53 | 49.56 | 89 | 0 | 0 1.2.24 | | 28.13 | 55.57 | 82 | 4.7 | 1.75 1.2.76 | | 27.78 | 42.74 | 81 | 1.4 | 0.4 1.2.48 | | 26.75 | 49.29 | 78 | 0 | 0 1.2.31 | | 25.72 | 38.12 | 75 | 1.57 | 0.34 1.2.5 | | 25.04 | 42.19 | 73 | 0 | 0 1.2.90 | | 19.55 | 36.76 | 57 | 0 | 0 1.2.99 | | 19.55 | 33.23 | 57 | 0 | 0 1.2.62 | | 19.21 | 37.64 | 56 | 0 | 0 1.2.92 | | 19.21 | 45.85 | 56 | 0 | 0 1.2.9 | | 17.15 | 35.89 | 50 | 0 | 0 1.2.39 | | 17.15 | 27.86 | 50 | 0.7 | 0.2 1.2.73 | | 17.15 | 33.07 | 50 | 1.4 | 0.32 1.2.52 | | 16.81 | 29.07 | 49 | 0.7 | 0.1 1.2.37 | | 16.12 | 39.37 | 47 | 0 | 0 1.2.57 | | 16.12 | 35.42 | 47 | 0 | 0 1.2.14 | | 15.78 | 31.43 | 46 | 1.57 | 0.34 1.2.3 | | 15.43 | 25.17 | 45 | 0.7 | 0.22 1.2.11 | | 15.09 | 29.18 | 44 | 0 | 0 1.2.54 | | 15.09 | 29.18 | 44 | 0 | 0 1.2.68 | | 14.75 | 24.39 | 43 | 0.7 | 0.2 1.2.66 | | 14.06 | 31.51 | 41 | 0 | 0 1.2.2 | | 13.72 | 20.49 | 40 | 1.57 | 0.5 1.2.88 | | 13.72 | 20.95 | 40 | 0.99 | 0.22 1.2.23 | | 13.38 | 20.27 | 39 | 1.4 | 0.28 1.2.34 | | 13.38 | 28.48 | 39 | 0 | 0 1.2.56 | | 13.38 | 28.48 | 39 | 0 | 0 1.2.82 | | 13.03 | 28.47 | 38 | 0 | 0 1.2.71 | | 12.35 | 30.77 | 36 | 0 | 0 1.2.67 | | 12 | 24.8 | 35 | 0 | 0 1.2.63 | | 10.98 | 20.44 | 32 | 1.71 | 0.9 1.2.1 | | 9.95 | 24.86 | 29 | 1.71 | 0.78 1.2.19 | | 9.6 | 21.06 | 28 | 0 | 0 1.2.22 | | 9.6 | 21.06 | 28 | 0 | 0 1.2.28 | | 9.6 | 21.06 | 28 | 0 | 0 1.2.46 | | 9.6 | 21.06 | 28 | 0 | 0 1.2.75 | | 9.6 | 21.06 | 28 | 0 | 0 1.2.35 | | 9.26 | 17.59 | 27 | 0.7 | 0.13 1.2.15 | | 8.92 | 11.44 | 26 | 0.7 | 0.11 1.2.36 | | 8.23 | 21.46 | 24 | 0.99 | 0.37 1.2.86 | | 7.89 | 17.5 | 23 | 1.98 | 0.89 1.2.4 | | 7.2 | 14.18 | 21 | 1.4 | 0.58 1.2.98 | | 6.86 | 13.59 | 20 | 0.99 | 0.34 1.2.6 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.10 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.13 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.18 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.21 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.25 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.40 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.42 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.50 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.51 | | 6.52 | 11.65 | 19 | 0.7 | 0.26 1.2.59 | | 6.52 | 13.56 | 19 | 0 | 0 1.2.64 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.65 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.74 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.81 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.87 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.91 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.94 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.95 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.96 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.97 | | 6.52 | 18.31 | 19 | 0 | 0 1.2.26 | | 5.83 | 12.83 | 17 | 0.7 | 0.16 1.2.32 | | 5.49 | 12.83 | 16 | 0.7 | 0.09 Populating font family aliases took 132 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > view #1.2.45 @< 3.5 > zoom 0.75 moved plane near -29.545798891320946 [-0.00277775 -0.01561962 0.99987415] moved plane far -29.545798891320946 [-0.00277775 -0.01561962 0.99987415] > surface #1.2.1-99 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.45 probeRadius 1.2 > select #1.2.45 3895 atoms, 1 residue, 1 model selected > kvfinder probeIn 1.2 probeOut 5.5 119 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.53 | | 1452.6 | 986.2 | 6725 | 0 | 0 1.2.36 | | 1282.61 | 1010.48 | 5938 | 8.09 | 1.82 1.2.9 | | 1234.87 | 969.38 | 5717 | 7.78 | 1.78 1.2.67 | | 1225.8 | 969.93 | 5675 | 7.73 | 1.77 1.2.81 | | 773.93 | 491.7 | 3583 | 9.6 | 2.27 1.2.26 | | 758.16 | 509.2 | 3510 | 9.6 | 2.27 1.2.54 | | 753.41 | 498.41 | 3488 | 9.08 | 2.32 1.2.100 | | 213.62 | 237.53 | 989 | 0 | 0 1.2.16 | | 201.1 | 162.73 | 931 | 2.68 | 0.63 1.2.66 | | 200.45 | 129.13 | 928 | 2.81 | 0.66 1.2.94 | | 193.97 | 146.98 | 898 | 3.23 | 0.78 1.2.59 | | 158.33 | 136.56 | 733 | 3.06 | 0.94 1.2.18 | | 118.58 | 120.07 | 549 | 0 | 0 1.2.45 | | 116.64 | 142.22 | 540 | 6.21 | 1.94 1.2.8 | | 116.42 | 135.11 | 539 | 0 | 0 1.2.73 | | 116.21 | 114.79 | 538 | 0 | 0 1.2.82 | | 115.78 | 133.7 | 536 | 0 | 0 1.2.93 | | 114.26 | 136.42 | 529 | 0 | 0 1.2.11 | | 92.02 | 89.95 | 426 | 3.93 | 1.17 1.2.111 | | 91.15 | 89.25 | 422 | 3.5 | 1.07 1.2.19 | | 90.5 | 115.36 | 419 | 0 | 0 1.2.64 | | 81 | 105.96 | 375 | 0 | 0 1.2.57 | | 79.7 | 84.23 | 369 | 3.7 | 1.02 1.2.101 | | 68.69 | 87.05 | 318 | 4.53 | 1.32 1.2.35 | | 65.88 | 83.86 | 305 | 3.06 | 0.95 1.2.92 | | 54.65 | 73.8 | 253 | 4.87 | 1.81 1.2.34 | | 46.66 | 54.94 | 216 | 2.4 | 0.55 1.2.102 | | 44.71 | 65.15 | 207 | 4.53 | 1.55 1.2.72 | | 39.74 | 58.58 | 184 | 0 | 0 1.2.1 | | 36.29 | 52.69 | 168 | 4.02 | 1.16 1.2.10 | | 35.64 | 54.18 | 165 | 3.45 | 0.97 1.2.25 | | 34.78 | 52.69 | 161 | 1.7 | 0.33 1.2.91 | | 31.97 | 45.94 | 148 | 0 | 0 1.2.31 | | 31.75 | 46.4 | 147 | 0 | 0 1.2.22 | | 30.67 | 37.43 | 142 | 1.7 | 0.45 1.2.117 | | 30.24 | 46.36 | 140 | 3.65 | 0.82 1.2.32 | | 30.02 | 45.33 | 139 | 0 | 0 1.2.78 | | 28.3 | 37.68 | 131 | 1.2 | 0.31 1.2.109 | | 28.08 | 42.49 | 130 | 0 | 0 1.2.90 | | 27.43 | 40 | 127 | 1.8 | 0.43 1.2.118 | | 27.22 | 40.43 | 126 | 0 | 0 1.2.15 | | 26.57 | 39.09 | 123 | 1.9 | 0.45 1.2.44 | | 26.57 | 39.16 | 123 | 1.2 | 0.25 1.2.63 | | 26.14 | 37.52 | 121 | 1.2 | 0.29 1.2.105 | | 25.49 | 31.17 | 118 | 1.34 | 0.38 1.2.58 | | 25.06 | 38.23 | 116 | 0 | 0 1.2.4 | | 24.62 | 32.12 | 114 | 1.34 | 0.4 1.2.6 | | 24.62 | 37.04 | 114 | 0 | 0 1.2.68 | | 21.82 | 38.38 | 101 | 0 | 0 1.2.99 | | 20.3 | 32.08 | 94 | 2.81 | 1.07 1.2.12 | | 20.09 | 34.05 | 93 | 0 | 0 1.2.76 | | 20.09 | 32.25 | 93 | 3.12 | 1.52 1.2.85 | | 19.66 | 35.41 | 91 | 1.8 | 0.51 1.2.62 | | 19.44 | 29.35 | 90 | 1.2 | 0.29 1.2.119 | | 17.93 | 28.88 | 83 | 0.85 | 0.31 1.2.13 | | 16.63 | 28.37 | 77 | 0 | 0 1.2.38 | | 16.42 | 29.42 | 76 | 0 | 0 1.2.65 | | 16.2 | 27.33 | 75 | 0 | 0 1.2.107 | | 16.2 | 27.01 | 75 | 0 | 0 1.2.110 | | 15.77 | 27.01 | 73 | 0 | 0 1.2.20 | | 15.55 | 26.2 | 72 | 0 | 0 1.2.2 | | 14.26 | 26.44 | 66 | 2.08 | 0.71 1.2.70 | | 14.26 | 26.1 | 66 | 0 | 0 1.2.103 | | 14.04 | 25.79 | 65 | 1.99 | 0.67 1.2.79 | | 13.18 | 23.81 | 61 | 0 | 0 1.2.48 | | 12.96 | 23.79 | 60 | 0.6 | 0.18 1.2.49 | | 12.96 | 25.2 | 60 | 0 | 0 1.2.52 | | 12.74 | 19.36 | 59 | 1.2 | 0.35 1.2.104 | | 12.1 | 20.14 | 56 | 0.6 | 0.18 1.2.39 | | 11.66 | 22.63 | 54 | 0 | 0 1.2.74 | | 11.66 | 21.34 | 54 | 0 | 0 1.2.98 | | 11.66 | 21.02 | 54 | 0 | 0 1.2.80 | | 11.02 | 20.14 | 51 | 0 | 0 1.2.112 | | 11.02 | 20.14 | 51 | 0 | 0 1.2.41 | | 10.37 | 17.27 | 48 | 0.6 | 0.14 1.2.89 | | 10.37 | 20.05 | 48 | 0 | 0 1.2.83 | | 10.15 | 19.57 | 47 | 1.47 | 0.47 1.2.108 | | 9.94 | 15.03 | 46 | 1.34 | 0.37 1.2.87 | | 9.72 | 18.43 | 45 | 0 | 0 1.2.75 | | 9.29 | 14.57 | 43 | 1.47 | 0.43 1.2.40 | | 8.64 | 16.75 | 40 | 0.6 | 0.11 1.2.106 | | 8.64 | 15.84 | 40 | 1.8 | 0.61 1.2.96 | | 7.99 | 13.44 | 37 | 0.85 | 0.26 1.2.21 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.23 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.27 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.30 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.50 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.56 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.60 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.114 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.115 | | 7.78 | 15.52 | 36 | 0 | 0 1.2.3 | | 7.56 | 14.41 | 35 | 1.47 | 0.62 1.2.5 | | 7.34 | 14.46 | 34 | 1.8 | 0.88 1.2.47 | | 7.34 | 13.03 | 34 | 0.6 | 0.16 1.2.55 | | 7.13 | 12.71 | 33 | 0.85 | 0.38 1.2.61 | | 7.13 | 12.05 | 33 | 0.6 | 0.22 1.2.69 | | 7.13 | 14.87 | 33 | 0.6 | 0.05 1.2.37 | | 6.48 | 11.65 | 30 | 0.6 | 0.2 1.2.113 | | 6.48 | 12.75 | 30 | 0.6 | 0.12 1.2.24 | | 6.26 | 11.56 | 29 | 0.6 | 0.19 1.2.7 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.14 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.17 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.28 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.29 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.33 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.43 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.46 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.51 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.71 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.84 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.86 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.88 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.95 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.97 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.116 | | 5.83 | 12.3 | 27 | 0 | 0 1.2.42 | | 5.62 | 11.73 | 26 | 1.8 | 0.88 1.2.77 | | 5.18 | 10.51 | 24 | 0.6 | 0.08 > view #1.2.53 @< 3.5 > zoom 0.75 moved plane near -34.0078564350414 [ 0.11252654 -0.05074317 0.99235221] moved plane far -34.0078564350414 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-119 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.53 probeRadius 1.2 > select #1.2.53 6725 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.5 105 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.32 | | 1482.75 | 1191.35 | 2896 | 7.96 | 1.73 1.2.46 | | 1480.7 | 992.57 | 2892 | 0 | 0 1.2.9 | | 1402.37 | 1084.63 | 2739 | 7.07 | 1.6 1.2.56 | | 1333.25 | 1065.59 | 2604 | 7.55 | 1.68 1.2.67 | | 904.7 | 560.43 | 1767 | 9.6 | 2.27 1.2.23 | | 869.38 | 584.26 | 1698 | 9.6 | 2.22 1.2.35 | | 826.37 | 547.66 | 1614 | 10.4 | 2.3 1.2.54 | | 284.16 | 197.04 | 555 | 3.3 | 0.7 1.2.75 | | 282.62 | 200.95 | 552 | 3.3 | 0.82 1.2.15 | | 270.85 | 187.44 | 529 | 2.99 | 0.67 1.2.17 | | 224.26 | 261.35 | 438 | 0 | 0 1.2.49 | | 202.24 | 165.99 | 395 | 2.77 | 1 1.2.8 | | 137.73 | 179.02 | 269 | 0 | 0 1.2.62 | | 136.7 | 141.34 | 267 | 0 | 0 1.2.69 | | 128.51 | 150.88 | 251 | 0 | 0 1.2.74 | | 127.49 | 142.35 | 249 | 0 | 0 1.2.83 | | 125.44 | 131.31 | 245 | 0 | 0 1.2.84 | | 122.37 | 162.55 | 239 | 6.5 | 2.46 1.2.99 | | 111.62 | 103.14 | 218 | 3.75 | 1.2 1.2.36 | | 102.4 | 126.99 | 200 | 4.08 | 1.19 1.2.12 | | 100.35 | 93.03 | 196 | 3.67 | 1.19 1.2.47 | | 95.74 | 99.25 | 187 | 3.67 | 0.96 1.2.52 | | 86.02 | 121.15 | 168 | 0 | 0 1.2.31 | | 85.5 | 106.14 | 167 | 2.65 | 1.05 1.2.76 | | 65.54 | 85.2 | 128 | 5.12 | 1.76 1.2.30 | | 61.95 | 80.86 | 121 | 4 | 0.78 1.2.89 | | 60.93 | 80.18 | 119 | 0 | 0 1.2.80 | | 59.9 | 93.82 | 117 | 5.12 | 1.91 1.2.21 | | 45.57 | 68.06 | 89 | 1.13 | 0.18 1.2.2 | | 45.06 | 72.49 | 88 | 4.08 | 1.37 1.2.51 | | 45.06 | 55.03 | 88 | 1.39 | 0.35 1.2.20 | | 44.54 | 48.97 | 87 | 2.26 | 0.5 1.2.73 | | 43.52 | 67.76 | 85 | 0 | 0 1.2.27 | | 37.89 | 57.45 | 74 | 0 | 0 1.2.60 | | 35.33 | 54.21 | 69 | 0 | 0 1.2.7 | | 33.79 | 49.17 | 66 | 0 | 0 1.2.42 | | 33.28 | 51.17 | 65 | 0 | 0 1.2.45 | | 33.28 | 56 | 65 | 0 | 0 1.2.103 | | 33.28 | 44.53 | 65 | 1.79 | 0.43 1.2.28 | | 32.77 | 54.5 | 64 | 0 | 0 1.2.70 | | 31.23 | 47.94 | 61 | 1.6 | 0.39 1.2.72 | | 30.21 | 45.98 | 59 | 1.6 | 0.39 1.2.87 | | 30.21 | 33.5 | 59 | 1.6 | 0.37 1.2.104 | | 30.21 | 47.91 | 59 | 0 | 0 1.2.48 | | 29.18 | 51.75 | 57 | 0 | 0 1.2.14 | | 28.67 | 41.42 | 56 | 1.6 | 0.39 1.2.82 | | 28.16 | 43.91 | 55 | 3.49 | 1.7 1.2.10 | | 27.65 | 47.81 | 54 | 0 | 0 1.2.37 | | 27.14 | 46.63 | 53 | 3.58 | 1.17 1.2.16 | | 26.62 | 42.83 | 52 | 3.39 | 1.26 1.2.41 | | 26.62 | 37.98 | 52 | 1.6 | 0.42 1.2.53 | | 25.09 | 31.86 | 49 | 1.13 | 0.35 1.2.91 | | 24.58 | 40.25 | 48 | 0.8 | 0.08 1.2.92 | | 24.58 | 36.56 | 48 | 1.79 | 0.43 1.2.65 | | 23.55 | 41.54 | 46 | 3.49 | 1.92 1.2.90 | | 23.55 | 37.36 | 46 | 0 | 0 1.2.6 | | 22.02 | 29.22 | 43 | 0.8 | 0.26 1.2.58 | | 20.99 | 41.3 | 41 | 0 | 0 1.2.97 | | 19.46 | 42.8 | 38 | 0 | 0 1.2.57 | | 17.41 | 31.94 | 34 | 0.8 | 0.19 1.2.66 | | 16.38 | 37.59 | 32 | 0 | 0 1.2.105 | | 16.38 | 30.33 | 32 | 0.8 | 0.12 1.2.3 | | 15.36 | 25.11 | 30 | 1.6 | 0.64 1.2.63 | | 15.36 | 32.54 | 30 | 0 | 0 1.2.95 | | 15.36 | 32.54 | 30 | 0 | 0 1.2.13 | | 14.34 | 27.51 | 28 | 0 | 0 1.2.55 | | 14.34 | 27.51 | 28 | 0 | 0 1.2.11 | | 13.31 | 21.48 | 26 | 1.39 | 0.54 1.2.50 | | 13.31 | 21.49 | 26 | 1.39 | 0.39 1.2.102 | | 13.31 | 31.52 | 26 | 3.39 | 1.76 1.2.100 | | 12.8 | 20.65 | 25 | 0.8 | 0.16 1.2.29 | | 12.29 | 17.9 | 24 | 0 | 0 1.2.64 | | 11.78 | 18.64 | 23 | 1.39 | 0.54 1.2.5 | | 11.26 | 20.6 | 22 | 0.8 | 0.18 1.2.1 | | 10.75 | 17.06 | 21 | 0.8 | 0.19 1.2.33 | | 10.75 | 16.52 | 21 | 0.8 | 0.27 1.2.4 | | 10.24 | 18.57 | 20 | 0 | 0 1.2.25 | | 10.24 | 17.92 | 20 | 0.8 | 0.04 1.2.18 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.19 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.22 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.24 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.26 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.34 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.39 | | 9.73 | 16.04 | 19 | 0.8 | 0.08 1.2.43 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.59 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.68 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.71 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.79 | | 9.73 | 16.33 | 19 | 0.8 | 0.21 1.2.81 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.88 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.101 | | 9.73 | 23.91 | 19 | 0 | 0 1.2.38 | | 8.19 | 14.91 | 16 | 0 | 0 1.2.78 | | 8.19 | 13.26 | 16 | 0.8 | 0.2 1.2.86 | | 8.19 | 13.77 | 16 | 0 | 0 1.2.96 | | 7.68 | 15.82 | 15 | 0.8 | 0.43 1.2.61 | | 7.17 | 12.54 | 14 | 0 | 0 1.2.77 | | 6.14 | 11.47 | 12 | 0.8 | 0.07 1.2.85 | | 5.63 | 9.78 | 11 | 0.8 | 0.15 1.2.40 | | 5.12 | 9.16 | 10 | 0 | 0 1.2.44 | | 5.12 | 10.46 | 10 | 0.8 | 0.16 1.2.93 | | 5.12 | 8.76 | 10 | 0 | 0 1.2.94 | | 5.12 | 10.21 | 10 | 0 | 0 1.2.98 | | 5.12 | 7.45 | 10 | 0 | 0 > view #1.2.46 @< 3.5 > zoom 0.75 moved plane near -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221] moved plane far -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-105 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.46 probeRadius 1.2 > select #1.2.46 2892 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.5 volumeCutoff 900 5 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1482.75 | 1191.35 | 2896 | 7.96 | 1.73 1.2.3 | | 1480.7 | 992.57 | 2892 | 0 | 0 1.2.1 | | 1402.37 | 1084.63 | 2739 | 7.07 | 1.6 1.2.4 | | 1333.25 | 1065.59 | 2604 | 7.55 | 1.68 1.2.5 | | 904.7 | 560.43 | 1767 | 9.6 | 2.27 > view #1.2.3 @< 3.5 > zoom 0.75 moved plane near -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221] moved plane far -32.39149791328405 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-5 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.3 probeRadius 1.2 > select #1.2.3 2892 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.4 volumeCutoff 900 4 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.3 | | 1565.7 | 1112.59 | 3058 | 0 | 0 1.2.2 | | 1387.52 | 1082.76 | 2710 | 7.96 | 1.77 1.2.4 | | 1288.7 | 1025.31 | 2517 | 7.63 | 1.68 1.2.1 | | 1260.54 | 986.31 | 2462 | 7.07 | 1.64 > view #1.2.3 @< 3.5 > zoom 0.75 moved plane near -34.221898520410825 [ 0.11252654 -0.05074317 0.99235221] moved plane far -34.221898520410825 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-4 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.3 probeRadius 1.2 > select #1.2.3 3058 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.6 volumeCutoff 900 6 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1545.22 | 1218.6 | 3018 | 7.92 | 1.72 1.2.1 | | 1498.62 | 1139.68 | 2927 | 7.71 | 1.67 1.2.4 | | 1492.48 | 1015.74 | 2915 | 0 | 0 1.2.5 | | 1458.18 | 1156.63 | 2848 | 7.71 | 1.64 1.2.3 | | 927.23 | 583.74 | 1811 | 9.6 | 2.42 1.2.6 | | 920.58 | 572.46 | 1798 | 9.6 | 2.23 > view #1.2.4 @< 3.5 > zoom 0.75 moved plane near -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221] moved plane far -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-6 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.4 probeRadius 1.2 > select #1.2.4 2915 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.6 volumeCutoff 900 6 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1545.22 | 1218.6 | 3018 | 7.92 | 1.72 1.2.1 | | 1498.62 | 1139.68 | 2927 | 7.71 | 1.67 1.2.4 | | 1492.48 | 1015.74 | 2915 | 0 | 0 1.2.5 | | 1458.18 | 1156.63 | 2848 | 7.71 | 1.64 1.2.3 | | 927.23 | 583.74 | 1811 | 9.6 | 2.42 1.2.6 | | 920.58 | 572.46 | 1798 | 9.6 | 2.23 > view #1.2.1 @< 3.5 > zoom 0.75 moved plane near -46.651350154162884 [ 0.11252654 -0.05074317 0.99235221] moved plane far -46.651350154162884 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-6 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.1 probeRadius 1.2 > select #1.2.1 2927 atoms, 1 residue, 1 model selected > view #!1.2.2 @< 3.5 > zoom 0.75 moved plane near -46.99354999206374 [ 0.11252654 -0.05074317 0.99235221] moved plane far -46.99354999206374 [ 0.11252654 -0.05074317 0.99235221] > ~surface #1.2 > surface #!1.2.2 probeRadius 1.2 > select #!1.2.2 3018 atoms, 1 residue, 1 model selected > view #!1.2.4 @< 3.5 > zoom 0.75 moved plane near -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221] moved plane far -30.619789271527594 [ 0.11252654 -0.05074317 0.99235221] > ~surface #1.2 > surface #!1.2.4 probeRadius 1.2 > select #!1.2.4 2915 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.3 volumeCutoff 900 5 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.3 | | 1472 | 957.8 | 2875 | 0 | 0 1.2.2 | | 1357.82 | 1074.91 | 2652 | 7.96 | 1.74 1.2.1 | | 1310.72 | 1054.59 | 2560 | 7.02 | 1.65 1.2.4 | | 1305.6 | 1063.38 | 2550 | 7.59 | 1.71 1.2.5 | | 927.74 | 631.71 | 1812 | 8.65 | 2.09 > view #1.2.3 @< 3.5 > zoom 0.75 moved plane near -30.3815091799255 [ 0.11252654 -0.05074317 0.99235221] moved plane far -30.3815091799255 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-5 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.3 probeRadius 1.2 > select #1.2.3 2875 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5.2 volumeCutoff 900 4 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.3 | | 1474.05 | 974 | 2879 | 0 | 0 1.2.2 | | 1281.02 | 1010.48 | 2502 | 7.96 | 1.72 1.2.1 | | 1243.14 | 1004.12 | 2428 | 6.97 | 1.62 1.2.4 | | 1183.74 | 947.83 | 2312 | 7.59 | 1.66 > view #1.2.3 @< 3.5 > zoom 0.75 moved plane near -31.01868138775968 [ 0.11252654 -0.05074317 0.99235221] moved plane far -31.01868138775968 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-4 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.3 probeRadius 1.2 > select #1.2.3 2879 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.2 probeOut 5 volumeCutoff 900 4 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.3 | | 1541.12 | 1046.49 | 3010 | 0 | 0 1.2.2 | | 1272.83 | 987.49 | 2486 | 7.71 | 1.68 1.2.1 | | 1171.97 | 950.57 | 2289 | 6.88 | 1.58 1.2.4 | | 1166.85 | 918.55 | 2279 | 7.2 | 1.61 > view #1.2.3 @< 3.5 > zoom 0.75 moved plane near -33.50697070131426 [ 0.11252654 -0.05074317 0.99235221] moved plane far -33.50697070131426 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-4 probeRadius 1.2 transparency 50 > ~surface #1.2 > surface #1.2.3 probeRadius 1.2 > select #1.2.3 3010 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 5 volumeCutoff 900 3 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1277.44 | 787.49 | 2495 | 0 | 0 1.2.1 | | 1125.38 | 907.04 | 2198 | 7.71 | 1.65 1.2.3 | | 1029.12 | 851.68 | 2010 | 5.99 | 1.48 > view #1.2.2 @< 3.5 > zoom 0.75 moved plane near -25.94895592629877 [ 0.11252654 -0.05074317 0.99235221] moved plane far -25.94895592629877 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-3 probeRadius 1.3 transparency 50 > ~surface #1.2 > surface #1.2.2 probeRadius 1.3 > select #1.2.2 2495 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 4.8 volumeCutoff 900 0 cavities found for 6x15 #1 > kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 4.9 volumeCutoff 900 2 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1277.95 | 792.67 | 2496 | 0 | 0 1.2.1 | | 1039.87 | 848.06 | 2031 | 6.84 | 1.6 > view #1.2.2 @< 3.5 > zoom 0.75 moved plane near -26.20204210646268 [ 0.11252654 -0.05074317 0.99235221] moved plane far -26.20204210646268 [ 0.11252654 -0.05074317 0.99235221] > surface #1.2.1-2 probeRadius 1.3 transparency 50 > ~surface #1.2 > surface #1.2.2 probeRadius 1.3 > select #1.2.2 2496 atoms, 1 residue, 1 model selected > view #!1.2.1 @< 3.5 > zoom 0.75 moved plane near -40.1437939466313 [-0.02399375 0.07662399 0.99677132] moved plane far -40.1437939466313 [-0.02399375 0.07662399 0.99677132] > ~surface #1.2 > surface #!1.2.1 probeRadius 1.3 > select #!1.2.1 2031 atoms, 1 residue, 1 model selected > view #!1.2.2 @< 3.5 > zoom 0.75 moved plane near -26.37070356607748 [-0.02399375 0.07662399 0.99677132] moved plane far -26.37070356607748 [-0.02399375 0.07662399 0.99677132] > ~surface #1.2 > surface #!1.2.2 probeRadius 1.3 > select #!1.2.2 2496 atoms, 1 residue, 1 model selected > kvfinder gridSpacing 0.8 probeIn 1.3 probeOut 4.9 volumeCutoff 900 2 cavities found for 6x15 #1 6x15 Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 1.2.2 | | 1277.95 | 792.67 | 2496 | 0 | 0 1.2.1 | | 1039.87 | 848.06 | 2031 | 6.84 | 1.6 > view #1.2.2 @< 3.5 > zoom 0.75 moved plane near -26.37070356607748 [-0.02399375 0.07662399 0.99677132] moved plane far -26.37070356607748 [-0.02399375 0.07662399 0.99677132] > surface #1.2.1-2 probeRadius 1.3 transparency 50 > ~surface #1.2 > surface #1.2.2 probeRadius 1.3 > select #1.2.2 2496 atoms, 1 residue, 1 model selected > select #!1 & (#!1.2.2 @< 3.5) 186 atoms, 154 bonds, 38 residues, 1 model selected > ~select #!1.2.2 186 atoms, 154 bonds, 38 residues, 1 model selected > ~surface #1.2 > view #1 > view #!1.2.2 @< 3.5 > zoom 0.75 moved plane near -25.504779775329137 [0.03552242 0.01945198 0.99917955] moved plane far -25.504779775329137 [0.03552242 0.01945198 0.99917955] > show > #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190 > hide > #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190 > show > #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190 > hide > #!1/A,C:60,63,142-143,146-147,157,161,183,186-187,190/B:60,63-64,142-143,146-147,157,161,183,186-187,190 > ~select #!1 & (#!1.2.2 @< 3.5) Nothing selected > select #!1 & (#!1.2.2 @< 3.5) 186 atoms, 154 bonds, 38 residues, 1 model selected > show sel atoms > hide sel atoms > ~select #!1 & (#!1.2.2 @< 3.5) Nothing selected > select #!1.2.2 2496 atoms, 1 residue, 1 model selected > ~surface #1.2 > surface #!1.2.2 probeRadius 1.3 > color byattribute a:kvfinder_depth #!1.2.1 2031 atoms, 1 residues, 1 surfaces, atom kvfinder_depth range 0 to 6.84 > select subtract #1.2.2 1 model selected > select add #1.2.1 2031 atoms, 1 residue, 1 model selected > delete sel > view #!1.2.2 @< 3.5 > zoom 0.75 moved plane near -25.504779775329137 [0.03552242 0.01945198 0.99917955] moved plane far -25.504779775329137 [0.03552242 0.01945198 0.99917955] > ~surface #1.2 > surface #!1.2.2 probeRadius 1.3 > select #!1.2.2 2496 atoms, 1 residue, 1 model selected > save > /Users/morgandooley/Documents/GltPh_Oligomerization/GltPh_structure_file.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 226, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 373, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 1058, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 741, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [, , , , ] -> -> 'cavity 1': Error while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1' ValueError: error processing: 'tools' -> [, , , , ] -> -> 'cavity 1': Error while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1' File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 226, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 373, in take_snapshot 'positions': self.positions.array(), ^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'array' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 127, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 138, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 62, in display run(session, cmd) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 1058, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 741, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [, , , , ] -> -> 'cavity 1': Error while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1' ValueError: error processing: 'tools' -> [, , , , ] -> -> 'cavity 1': Error while saving session data for 'tools' -> [, , , , ] -> -> 'cavity 1' File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( See log for complete Python traceback. Failed to send bug report. Error while sending follows: Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/bug_reporter/tool.py"", line 253, in submit errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields, timeout=10) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/webservices/post_form.py"", line 45, in post_multipart_formdata return r.status, r.msg, r.getheaders(), r.read() ^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 482, in read s = self._safe_read(self.length) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 633, in _safe_read raise IncompleteRead(data, amt-len(data)) http.client.IncompleteRead: IncompleteRead(666 bytes read, 6446 more expected) OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,7 Model Number: MX2Y3LL/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 48 GB System Firmware Version: 13822.61.10 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.3 (24G419) Kernel Version: Darwin 24.6.0 Time since boot: 54 days, 6 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 narwhals: 2.22.1 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 2.4.6 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.2 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tomlkit: 0.15.0 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Surface/Binding Analysis duplicate all ChimeraX