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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.