Opened 3 years ago

Closed 3 years ago

#8169 closed defect (fixed)

Check Waters referencing dead pseudobond group?

Reported by: chimerax-bug-report@… 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 Eric Pettersen, 3 years ago

Component: UnassignedSessions
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCheck Waters referencing dead pseudobond group?

comment:2 by Eric Pettersen, 3 years ago

Resolution: fixed
Status: acceptedclosed

Close the tool if the user independently closes the H-bond groups, since the tool assumes in many places that the groups exist.

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