Opened 3 years ago
Closed 3 years ago
#8169 closed defect (fixed)
Check Waters referencing dead pseudobond group?
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sessions | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-12.2.1-arm64-arm-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/chimerax/OATP1B1-Fab19.cxs Log from Mon Dec 12 14:50:54 2022UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/ChimeraX/OATP1B3_FAB19/2022-12-09_OATP1B3-Fab19.cxs Opened j215ZR_1B3Fab19_final2.mrc as #2, grid size 512,512,512, pixel 0.51, shown at level 0.00664, step 1, values float32 Log from Fri Dec 9 13:40:36 2022You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > show cartoons > open /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/OATP1B3-Fab19_apo_ata- > coot-74.pdb Chain information for OATP1B3-Fab19_apo_ata-coot-74.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > open /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/j215ZR_1B3Fab19_final2.mrc Opened j215ZR_1B3Fab19_final2.mrc as #2, grid size 512,512,512, pixel 0.51, shown at level 0.00186, step 2, values float32 > volume #2 level 0.004603 > volume #2 color #898989 > volume #2 color #89898980 > volume #2 color #89898965 > volume #2 color #cfcfcf65 > volume #2 level 0.006047 > open 2bbv Summary of feedback from opening 2bbv fetched from pdb --- notes | Fetching compressed mmCIF 2bbv from http://files.rcsb.org/download/2bbv.cif Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif 2bbv title: The refined three-dimensional structure of an insect virus At 2.8 angstroms resolution [more info...] Chain information for 2bbv #3 --- Chain | Description | UniProt A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') | Non-standard residues in 2bbv #3 --- CA — calcium ion 2bbv mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame 6| crystal asymmetric unit, crystal frame > color bychain [Repeated 1 time(s)] > close #3 > style /b stick Changed 4043 atom styles > style /b stick Changed 4043 atom styles > ribbon /a > style stick Changed 5838 atom styles > style ball Changed 5838 atom styles > style ball Changed 5838 atom styles > style /b stick Changed 4043 atom styles > style /c stick Changed 970 atom styles > style /d stick Changed 769 atom styles > style /d stick Changed 769 atom styles > style /a stick Changed 56 atom styles > style /b stick Changed 4043 atom styles > volume #2 step 1 > volume #2 level 0.006637 > select add /B:427 7 atoms, 7 bonds, 1 residue, 1 model selected > select add /B:645 18 atoms, 18 bonds, 2 residues, 3 models selected > select add /B:532 29 atoms, 28 bonds, 3 residues, 3 models selected > select add /B:535 40 atoms, 39 bonds, 4 residues, 3 models selected > select add /B:448 47 atoms, 45 bonds, 5 residues, 3 models selected > select add /B:569 52 atoms, 49 bonds, 6 residues, 3 models selected > select add /B:568 61 atoms, 57 bonds, 7 residues, 1 model selected > select add /B:573 65 atoms, 60 bonds, 8 residues, 1 model selected > hide #!2 models > select add /B:417 73 atoms, 67 bonds, 9 residues, 1 model selected > select add /B:421 84 atoms, 78 bonds, 10 residues, 1 model selected > select clear > select add /B:421 11 atoms, 11 bonds, 1 residue, 1 model selected > select add /B:420 19 atoms, 18 bonds, 2 residues, 1 model selected > select add /B:422 28 atoms, 26 bonds, 3 residues, 1 model selected > select add /B:423 36 atoms, 33 bonds, 4 residues, 1 model selected > select add /B:424 44 atoms, 40 bonds, 5 residues, 1 model selected > select add /B:425 56 atoms, 52 bonds, 6 residues, 1 model selected > select add /B:426 67 atoms, 63 bonds, 7 residues, 1 model selected > style sel stick Changed 67 atom styles > style sel stick Changed 67 atom styles > style sel sphere Changed 67 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel ball Changed 67 atom styles > color sel byhetero [Repeated 1 time(s)] > rainbow sel [Repeated 1 time(s)] > hbonds sel reveal true 8 hydrogen bonds found > hbonds sel reveal true 8 hydrogen bonds found Alignment identifier is 1/B Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B > interfaces select & ~solvent Missing or invalid "atoms" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid "atoms" argument: invalid atoms specifier > surface #1 > color /n fromatoms > select clear > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting flat > lighting shadows true intensity 0.5 > lighting soft [Repeated 1 time(s)] > lighting simple [Repeated 1 time(s)] > lighting soft > hide #1.5 models > show #1.5 models > hide #1.3 models > show #1.3 models > hide #1.1 models > hide #1.2 models > show #1.2 models > hide #1.2 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.4 models > show #1.4 models > hide #1.4 models > view [Repeated 1 time(s)] > ui tool show "Side View" > set bgColor gray > set bgColor black > set bgColor white [Repeated 1 time(s)] > set bgColor gray > set bgColor black > set bgColor gray > set bgColor white > set bgColor gray > set bgColor black > hide surfaces > show surfaces > hide surfaces > show surfaces > hide surfaces > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > show #1.1 models > hide #1.1 models > show #1.2 models > hide #1.2 models > lighting flat [Repeated 1 time(s)] > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting simple > lighting soft > lighting simple > cartoon style (#1.3-5#!1 & coil) xsection oval > cartoon style #1.3-5#!1 xsection barbell modeHelix default > mlp Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > color bfactor 5838 atoms, 750 residues, 3 surfaces, atom bfactor range 0 to 90.1 > color bynucleotide [Repeated 1 time(s)] > hbonds reveal true 597 hydrogen bonds found > hbonds reveal true 597 hydrogen bonds found > ~hbonds > color byhetero [Repeated 1 time(s)] > color bychain > color bypolymer > rainbow > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > coulombic Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > mlp Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > mlp Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > hide #!1.5 models > hide #!1.4 models > hide #!1.3 models > show #1.3 models > color #1.3 #cfcfcf63 > show #1.4 models > hide #!1.4 models > show #1.4 models > hide #!1.4 models > show #1.4 models > color byhetero [Repeated 1 time(s)] > style ball Changed 5838 atom styles > color bychain > interfaces ~solvent 3 buried areas: C D 851, B C 831, B A 473 > interfaces ~solvent 3 buried areas: C D 851, B C 831, B A 473 > style sel stick Changed 497 atom styles > style sel stick Changed 497 atom styles > style sel sphere Changed 497 atom styles > style sel sphere Changed 497 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel surfaces [Repeated 1 time(s)] > hide sel surfaces [Repeated 2 time(s)] > hide sel cartoons > hide sel atoms [Repeated 1 time(s)] > show sel atoms > show sel cartoons > hide sel cartoons [Repeated 1 time(s)] > hide sel surfaces [Repeated 2 time(s)] > hide #!1 models > show #!1 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide sel surfaces [Repeated 5 time(s)] > hide #1.3 models > show #1.3 models > hide #1.4 models > show #1.4 models > hide #1.4 models > show #1.4 models > hide #1.4 models > show #1.4 models > hide #1.3 models > show #1.3 models > hide #1.5 models > show #1.5 models > hide #1.5 models > style sel sphere Changed 497 atom styles > style sel sphere Changed 497 atom styles > coulombic sel Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > rainbow sel [Repeated 1 time(s)] > mlp sel Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.3: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > show #1.1 models > show sel atoms [Repeated 1 time(s)] > hide sel atoms [Repeated 3 time(s)] > show sel cartoons [Repeated 1 time(s)] > hide sel cartoons [Repeated 1 time(s)] > show sel cartoons > set bgColor black > set bgColor white [Repeated 1 time(s)] > set bgColor black > lighting simple > lighting soft > lighting full > lighting soft > hide sel surfaces > color sel bychain > select clear > undo [Repeated 1 time(s)] > select clear > close #1 > open /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/OATP1B3-Fab19_apo_ata- > coot-74.pdb Chain information for OATP1B3-Fab19_apo_ata-coot-74.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > color bychain [Repeated 2 time(s)] > rainbow [Repeated 1 time(s)] > color bychain [Repeated 4 time(s)] > style sphere Changed 5838 atom styles > style sphere Changed 5838 atom styles > undo [Repeated 2 time(s)] > interfaces ~solvent 3 buried areas: C D 851, B C 831, B A 473 > style sel stick Changed 394 atom styles > style sel stick Changed 394 atom styles > hbonds sel reveal true 57 hydrogen bonds found Alignment identifier is 1/B Alignment identifier is 1/C > show sel atoms > select clear > select add /C:31@CB 1 atom, 1 residue, 1 model selected > select clear > select add /C:31@CG 1 atom, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select :sti Nothing selected > show sel atoms > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 16 contacting residues > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 16 contacting residues > select clear > color bychain [Repeated 1 time(s)] > lighting simple > lighting soft > lighting full > lighting flat > lighting soft > lighting flat > lighting soft > surface #1 > select clear > lighting flat > lighting soft > lighting simple [Repeated 1 time(s)] > lighting soft > hide #1.1 models > hide #!1.5 models > hide #1.4.1 models > show #1.4.1 models > hide #1.4.1 models > show #1.4.1 models > hide #1.3.2 models > show #1.3.2 models > hide #1.3.2 models > show #1.3.2 models > hide #1.3.1 models > show #1.3.1 models > hide #!1.3 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.1 models > hide #1.1 models > surface (#!1 & sel) > select clear > surface #1.3-4#!1 > hide #!1.4 models > hide #!1.5 models > style (#!1 & sel) sphere Changed 118 atom styles > select clear > style #1.3#!1 ball Changed 5838 atom styles > label #1.3#!1 text "{0.label_one_letter_code} {0.number}{0.insertion_code}" > undo > redo > ~label #1.3,6#!1 residues > label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}" > select clear > color (#!1 & sel) black > color (#!1 & sel) purple > color (#!1 & sel) medium blue > color (#!1 & sel) forest green > color (#!1 & sel) #fefff7ff > color (#!1 & sel) #fdfff8ff > color (#!1 & sel) #eefff2ff > color (#!1 & sel) #dfffeeff > color (#!1 & sel) #daffedff > color (#!1 & sel) #ccffe9ff > color (#!1 & sel) #c1ffe7ff > color (#!1 & sel) #bcffe5ff > color (#!1 & sel) #b3ffe2ff > color (#!1 & sel) #b0ffe1ff > color (#!1 & sel) #a8ffdeff > color (#!1 & sel) #a3ffdcff > color (#!1 & sel) #a0ffdbff > color (#!1 & sel) #98ffd8ff > color (#!1 & sel) #96ffd8ff > color (#!1 & sel) #94ffd7ff > color (#!1 & sel) #93ffd6ff > color (#!1 & sel) #92ffd5ff > color (#!1 & sel) #92ffd4ff > color (#!1 & sel) #91ffd3ff > color (#!1 & sel) #90ffd3ff > color (#!1 & sel) #8effd0ff > color (#!1 & sel) #8effcfff > color (#!1 & sel) #8bffc9ff > color (#!1 & sel) #88ffc6ff > color (#!1 & sel) #86ffc0ff > color (#!1 & sel) #84ffbcff > color (#!1 & sel) #81ffb7ff > color (#!1 & sel) #80ffb4ff > color (#!1 & sel) #7dffb1ff > color (#!1 & sel) #7dffb0ff > color (#!1 & sel) #7cffafff > color (#!1 & sel) #7bffaeff > color (#!1 & sel) #61ff94ff > color (#!1 & sel) #5eff8fff > color (#!1 & sel) #59ff8bff > color (#!1 & sel) #56ff86ff > color (#!1 & sel) #53ff85ff > color (#!1 & sel) #52ff83ff > color (#!1 & sel) #50ff82ff > color (#!1 & sel) #4dff80ff > color (#!1 & sel) #45ff7cff > color (#!1 & sel) #40ff7aff > color (#!1 & sel) #3dff79ff > color (#!1 & sel) #39ff78ff > color (#!1 & sel) #33ff76ff > color (#!1 & sel) #2fff77ff > color (#!1 & sel) #2aff76ff > color (#!1 & sel) #27ff77ff > color (#!1 & sel) #25ff76ff > color (#!1 & sel) #22ff76ff > color (#!1 & sel) #21ff75ff > color (#!1 & sel) #21ff74ff > color (#!1 & sel) #21ff73ff > color (#!1 & sel) #21ff49ff > color (#!1 & sel) #20ff44ff > color (#!1 & sel) #21ff42ff > color (#!1 & sel) #22ff3fff > color (#!1 & sel) #23ff3dff > color (#!1 & sel) #23ff3bff > color (#!1 & sel) #23ff39ff > color (#!1 & sel) #23ff38ff > color (#!1 & sel) #23ff37ff > color (#!1 & sel) #23ff35ff > color (#!1 & sel) #23ff33ff > color (#!1 & sel) #22ff2eff > color (#!1 & sel) #23ff2dff > color (#!1 & sel) #22ff2aff > color (#!1 & sel) #22ff28ff > color (#!1 & sel) #22ff27ff > color (#!1 & sel) #22ff25ff > color (#!1 & sel) #21ff22ff > color (#!1 & sel) #22ff21ff > color (#!1 & sel) #24ff21ff > color (#!1 & sel) #27ff21ff > color (#!1 & sel) #28ff21ff [Repeated 1 time(s)] > color (#!1 & sel) #28fe21ff > color (#!1 & sel) #27fb20ff > color (#!1 & sel) #20cf1bff > color (#!1 & sel) #20ca1aff > color (#!1 & sel) #1fc71aff > color (#!1 & sel) #1db918ff > color (#!1 & sel) #1cb517ff > color (#!1 & sel) #19a015ff > color (#!1 & sel) #199e14ff > color (#!1 & sel) #189914ff > color (#!1 & sel) #158811ff > color (#!1 & sel) #158411ff > color (#!1 & sel) #137b10ff > color (#!1 & sel) #13770fff > color (#!1 & sel) #12740fff > color (#!1 & sel) #12730fff > color (#!1 & sel) #12720fff > color (#!1 & sel) #12710eff > color (#!1 & sel) #12700eff > color (#!1 & sel) #116d0eff > color (#!1 & sel) #116a0eff > color (#!1 & sel) #10680dff > color (#!1 & sel) #0f620dff > color (#!1 & sel) #0f610cff > color (#!1 & sel) #0f5d0cff > color (#!1 & sel) #0e5b0cff > color (#!1 & sel) #0d560bff > color (#!1 & sel) #0d510aff > color (#!1 & sel) #0a3d08ff > color (#!1 & sel) #093907ff > color (#!1 & sel) #083607ff > color (#!1 & sel) #083507ff > color (#!1 & sel) #083407ff > color (#!1 & sel) #083307ff > color (#!1 & sel) #083206ff > color (#!1 & sel) #072f06ff [Repeated 1 time(s)] > color (#!1 & sel) #072c06ff [Repeated 1 time(s)] > color (#!1 & sel) #072d06ff [Repeated 1 time(s)] > color (#!1 & sel) #093c08ff > color (#!1 & sel) #0a3d08ff > color (#!1 & sel) #0a4208ff > color (#!1 & sel) #0b4409ff > color (#!1 & sel) #0b4509ff > color (#!1 & sel) #0b4a09ff > color (#!1 & sel) #0c4a0aff > color (#!1 & sel) #0c4b0aff [Repeated 1 time(s)] > color (#!1 & sel) #0d520bff > color (#!1 & sel) #0d530bff > color (#!1 & sel) #0d550bff > color (#!1 & sel) #0d560bff [Repeated 1 time(s)] > color (#!1 & sel) #0e5b0cff > color (#!1 & sel) #0e5c0cff [Repeated 1 time(s)] > color (#!1 & sel) #0f5d0cff [Repeated 1 time(s)] > color (#!1 & sel) #0f5e0cff > color (#!1 & sel) #0f600cff > color (#!1 & sel) #0f610cff [Repeated 2 time(s)] > color (#!1 & sel) #0f600cff > color (#!1 & sel) #0e5c0cff > color (#!1 & sel) #0e580bff [Repeated 1 time(s)] > select clear > cd /Users/anca-denise/Desktop/OATP1B3/1B3fab19MB/ChimeraX/OATP1B3_FAB19 Current working directory is: /Users/anca- denise/Desktop/OATP1B3/1B3fab19MB/ChimeraX/OATP1B3_FAB19 > save /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/ChimeraX/OATP1B3_FAB19/2022-12-09_OATP1B3-Fab19.cxs > includeMaps true ——— End of log from Fri Dec 9 13:40:36 2022 ——— opened ChimeraX session > set bgColor white > close #2 > hide #!1 models > show #!1 models > hide #!1.3 models > set bgColor black > lighting simple > hbonds reveal true 597 hydrogen bonds found > hide surfaces [Repeated 1 time(s)] > hide cartoons [Repeated 1 time(s)] > hide atoms > show cartoons > set bgColor white > set bgColor black > close session > open /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/OATP1B3-Fab19_apo_ata- > coot-74.pdb Chain information for OATP1B3-Fab19_apo_ata-coot-74.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available > set bgColor white > color bychain > hide #1.1 models Alignment identifier is 1/B Alignment identifier is 1/C Alignment identifier is 1/D Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B Destroying pre-existing alignment with identifier 1/C Alignment identifier is 1/C Destroying pre-existing alignment with identifier 1/D Alignment identifier is 1/D > interfaces ~solvent 3 buried areas: C D 851, B C 831, B A 473 > ui tool show "Side View" > lighting simple [Repeated 1 time(s)] > lighting soft > lighting simple > lighting soft [Repeated 1 time(s)] > lighting simple > lighting full > lighting simple [Repeated 1 time(s)] > hide atoms > show sel atoms > save /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/OATP1B1-Fab19.cxs ——— End of log from Mon Dec 12 14:50:54 2022 ——— opened ChimeraX session > interfaces select & ~solvent Missing or invalid "atoms" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid "atoms" argument: invalid atoms specifier > select clear [Repeated 1 time(s)] > interfaces ~solvent 3 buried areas: C D 851, B C 831, B A 473 > hbonds sel reveal true 23 hydrogen bonds found > hbonds sel reveal true 450 hydrogen bonds found > ui tool show Clashes > clashes ignoreHiddenModels true 8 clashes > clashes ignoreHiddenModels true 8 clashes > clashes ignoreHiddenModels true 8 clashes > hide #1.2 models > color #1 #e83d37ff > color #1 #c865e8ff > color #1 #c967e8ff > color #1.3 #11e7d6ff models > hide #1.3 models > show #1.3 models > ui tool show "Altloc Explorer" > ui tool show Contacts > contacts intraModel false intraMol false ignoreHiddenModels true No contacts > close #1.4 > ui tool show Contacts > ui tool show Distances > ui tool show H-Bonds > hbonds saltOnly true reveal true 7 hydrogen bonds found > hbonds saltOnly true reveal true 7 hydrogen bonds found > hbonds saltOnly true reveal true 7 hydrogen bonds found > hide #!1 models > show #!1 models > hide #1.3 models > select clear > show #1.1 models > hide #1.1 models > show #1.2 models > hide #1.2 models > show #1.2 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.3 models > save /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/chimerax/hbonds.cxs > rainbow > hide #1.2 models > show #1.2 models > ui tool show H-Bonds > hbonds saltOnly true reveal true 7 hydrogen bonds found > hbonds saltOnly true reveal true 7 hydrogen bonds found > hide #1.2 models > show #1.2 models > color #1.2 #fa231cff models > color #1.2 #fa2a0cff models > color #1.2 #fa3e2aff models > color #1.2 #fa4c3bff models > color #1.2 #ff4d3cff models > hbonds reveal true 597 hydrogen bonds found > ~hbonds > color bfactor 5838 atoms, 750 residues, atom bfactor range 0 to 90.1 > mlp Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface": minimum -26.63, mean -0.1899, maximum 24.26 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface": minimum -28.91, mean -5.257, maximum 23.44 Map values for surface "OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface": minimum -27.12, mean -5.841, maximum 22.56 To also show corresponding color key, enter the above mlp command and add key true > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.2: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > color bychain > hide #1.5 models > hide #1.4 models > coulombic Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.2: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > hide #1.5 models > hide #1.4 models > show #1.4 models > hide #1.4 models > show #1.4 models > hide #1.4 models > color bfactor 5838 atoms, 750 residues, 3 surfaces, atom bfactor range 0 to 90.1 > rainbow > coulombic Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_B SES surface #1.2: minimum, -32.41, mean 1.12, maximum 16.27 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_C SES surface #1.4: minimum, -12.20, mean -0.34, maximum 10.44 Coulombic values for OATP1B3-Fab19_apo_ata-coot-74.pdb_D SES surface #1.5: minimum, -9.91, mean 1.64, maximum 12.67 To also show corresponding color key, enter the above coulombic command and add key true > color bychain > hide #1.5 models > del:. /c Unknown command: del:. /c > delete:.c Unknown command: delete:.c > delete:.D Unknown command: delete:.D > delete:. D Unknown command: delete:. D > delete:. d Unknown command: delete:. d > select /D 769 atoms, 785 bonds, 1 pseudobond, 103 residues, 2 models selected > select clear > delete/ d Unknown command: delete/ d > delete /D > interfaces ~solvent 2 buried areas: B C 831, B A 473 > delete /A > interfaces ~solvent 1 buried areas: B C 831 > hide atoms > hide surfaces > hbonds sel reveal true 44 hydrogen bonds found > hide #1.5 models > ui tool show H-Bonds > hbonds saltOnly true reveal true 5 hydrogen bonds found > label (#!1 & sel) text "{0.label_one_letter_code} > {0.number}{0.insertion_code}" > hbonds sel reveal true 44 hydrogen bonds found > hbonds sel reveal true 44 hydrogen bonds found > ~hbonds > hbonds sel reveal true 44 hydrogen bonds found > select clear Drag select of 1 residues Drag select of 2 residues > select subtract /B:404 6 atoms, 2 pseudobonds, 1 residue, 3 models selected > select subtract /B:403 2 pseudobonds, 2 models selected > ~hbonds > hbonds reveal true 526 hydrogen bonds found > ~hbonds > hide #1.6 models > show #1.6 models > hide #1.2 models > show #1.2 models > show #1.3 models > hide #1.3 models > hide #1.4 models > show #1.4 models > style stick Changed 5013 atom styles > hide atoms > hbonds sel reveal true 39 hydrogen bonds found > hbonds sel reveal true 39 hydrogen bonds found > ~hbonds > ui tool show H-Bonds > hbonds intraModel false saltOnly true intraMol false intraRes false reveal > true 0 hydrogen bonds found > ui tool show "Check Waters" > hbonds interModel false reveal true restrict any name "water H-bonds" 526 hydrogen bonds found > ~select Nothing selected > ~hbonds [Repeated 1 time(s)] > hide #1.8 models > close #1.8 > close #1.7 > hide atoms > color byhetero [Repeated 1 time(s)] > interfaces ~solvent 0 buried areas: > hide #1.4 models > show #1.4 models > close #1.3 > hbonds sel reveal true 18 hydrogen bonds found > hbonds sel reveal true 23 hydrogen bonds found > hbonds sel reveal true 26 hydrogen bonds found > save /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/chimerax/interacting- > residues.cxs Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot 'category': self.name, File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 161, in _get_name return self._category File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 80, in get_prop cget(self._c_pointer_ref, 1, v_ref) AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 899, in save session.save(output, version=version, include_maps=include_maps) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 625, in save mgr.discovery(self._state_containers) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340>: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> ValueError: error processing: 'tools' -> -> -> : Error while saving session data for 'tools' -> -> -> File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot 'category': self.name, File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 161, in _get_name return self._category File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 80, in get_prop cget(self._c_pointer_ref, 1, v_ref) AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 51, in display run(session, cmd) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/Users/anca- denise/Desktop/ChimeraX-1.5.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 "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Users/anca- denise/Desktop/ChimeraX-1.5.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 "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py", line 90, in provider_save saver_info.save(session, path, **provider_kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py", line 84, in save return cxs_save(session, path, **kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 899, in save session.save(output, version=version, include_maps=include_maps) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 625, in save mgr.discovery(self._state_containers) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340>: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> ValueError: error processing: 'tools' -> -> -> : Error while saving session data for 'tools' -> -> -> File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/chimerax/interaction.cxs Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot 'category': self.name, File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 161, in _get_name return self._category File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 80, in get_prop cget(self._c_pointer_ref, 1, v_ref) AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 899, in save session.save(output, version=version, include_maps=include_maps) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 625, in save mgr.discovery(self._state_containers) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340>: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> ValueError: error processing: 'tools' -> -> -> : Error while saving session data for 'tools' -> -> -> File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot 'category': self.name, File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 161, in _get_name return self._category File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 80, in get_prop cget(self._c_pointer_ref, 1, v_ref) AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 51, in display run(session, cmd) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/Users/anca- denise/Desktop/ChimeraX-1.5.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 "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Users/anca- denise/Desktop/ChimeraX-1.5.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 "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py", line 90, in provider_save saver_info.save(session, path, **provider_kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py", line 84, in save return cxs_save(session, path, **kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 899, in save session.save(output, version=version, include_maps=include_maps) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 625, in save mgr.discovery(self._state_containers) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340>: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> ValueError: error processing: 'tools' -> -> -> : Error while saving session data for 'tools' -> -> -> File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save /Users/anca- > denise/Desktop/OATP1B3/1B3fab19MB/2.97A_TightMask/2.97_Corrected_Coordinates/KasparNotes/chimerax/1b3res.cxs Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot 'category': self.name, File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 161, in _get_name return self._category File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 80, in get_prop cget(self._c_pointer_ref, 1, v_ref) AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 899, in save session.save(output, version=version, include_maps=include_maps) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 625, in save mgr.discovery(self._state_containers) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340>: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> ValueError: error processing: 'tools' -> -> -> : Error while saving session data for 'tools' -> -> -> File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 298, in take_snapshot 'category': self.name, File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/pbgroup.py", line 161, in _get_name return self._category File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 80, in get_prop cget(self._c_pointer_ref, 1, v_ref) AttributeError: 'PseudobondGroup' object has no attribute '_c_pointer_ref' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process(obj, parents) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 116, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog _dlg.display(session, **kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py", line 51, in display run(session, cmd) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/Users/anca- denise/Desktop/ChimeraX-1.5.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 "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Users/anca- denise/Desktop/ChimeraX-1.5.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 "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py", line 90, in provider_save saver_info.save(session, path, **provider_kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py", line 84, in save return cxs_save(session, path, **kw) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 899, in save session.save(output, version=version, include_maps=include_maps) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 625, in save mgr.discovery(self._state_containers) File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340>: Error while saving session data for 'tools' -> <chimerax.core.tools.Tools object at 0x119525a60> -> <chimerax.check_waters.tool.CheckWaterViewer object at 0x15d0da7f0> -> <chimerax.atomic.pbgroup.PseudobondGroup object at 0x15cb73340> ValueError: error processing: 'tools' -> -> -> : Error while saving session data for 'tools' -> -> -> File "/Users/anca- denise/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac21,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 7429.81.3 OS Loader Version: 7429.81.3 Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 18 days 4:03 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 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: No Connection Type: Internal U28E850: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 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: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → Sessions |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Check Waters referencing dead pseudobond group? |
comment:2 by , 3 years ago
Resolution: | → fixed |
---|---|
Status: | accepted → closed |
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Close the tool if the user independently closes the H-bond groups, since the tool assumes in many places that the groups exist.