Opened 3 years ago

Closed 3 years ago

#7367 closed defect (duplicate)

Session save: function 'set_pbgroup_py_instance' not found

Reported by: jmreimer@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /Users/janicereimer/Dropbox/Chi_Lis1/Figures/Figure2_files/2B_phi_to_chi-
> centered.cxs

Opened cryosparc_P6_J841_006_volume_map_sharp.mrc as #1, grid size
352,352,352, pixel 1.31, shown at level 0.565, step 1, values float32  
Log from Mon Aug 1 16:50:47 2022

> cd /home/jmreimer/Desktop/Misc

Error running startup command 'cd /home/jmreimer/Desktop/Misc': Expected name
of a folder to open/read; a name of 'browse' will bring up a file browser or a
keyword  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/janicereimer/Documents/UCSD/Dynein/Chi_dynein_paper/cryosparc_P6_J841_006_volume_map_sharp.mrc

Opened cryosparc_P6_J841_006_volume_map_sharp.mrc as #1, grid size
352,352,352, pixel 1.31, shown at level 0.301, step 2, values float32  

> open
> /Users/janicereimer/Documents/UCSD/Dynein/chi_dynein_model/chi_aug1-2-coot-1.pdb

Chain information for chi_aug1-2-coot-1.pdb #2  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> transparency 50

> volume #1 step 1

> volume #1 level 0.3731

> surface dust #1 size 13.1

> volume #1 level 0.5649

> open "/Users/janicereimer/Downloads/5nug (1).pdb"

5nug (1).pdb title:  
Motor domains from human cytoplasmic dynein-1 In the φ-particle conformation
[more info...]  
  
Chain information for 5nug (1).pdb #3  
---  
Chain | Description | UniProt  
A B | cytoplasmic dynein 1 heavy chain 1 | DYHC1_HUMAN  
  
Non-standard residues in 5nug (1).pdb #3  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
  

> ui tool show Matchmaker

> matchmaker #!3 to #2/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker chi_aug1-2-coot-1.pdb, chain A (#2) with 5nug (1).pdb, chain A
(#3), sequence alignment score = 5397.7  
RMSD between 1271 pruned atom pairs is 1.368 angstroms; (across all 2348
pairs: 4.074)  
  

> matchmaker #!3 to #2/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker chi_aug1-2-coot-1.pdb, chain A (#2) with 5nug (1).pdb, chain A
(#3), sequence alignment score = 5397.7  
RMSD between 1271 pruned atom pairs is 1.368 angstroms; (across all 2348
pairs: 4.074)  
  

> hide atoms

> show cartoons

> hide #!1 models

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 98801 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> open /Users/janicereimer/Documents/UCSD/Dynein/chi_dynein_model/chi_aug1.pdb

Chain information for chi_aug1.pdb #4  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C F | No description available  
  

> close #4

> open
> /Users/janicereimer/Documents/UCSD/Dynein/chi_dynein_model/chi_aug1-1.pdb

Chain information for chi_aug1-1.pdb #4  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C F | No description available  
  

> close #4

> open
> /Users/janicereimer/Dropbox/Chi_Lis1/Deposition/dynein_sym_expand/dynein_local_july27-with-
> nucs-refined_045-noH-coot-2.pdb

Chain information for dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> ui tool show Matchmaker

> matchmaker #!4 to #3/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5nug (1).pdb, chain B (#3) with dynein_local_july27-with-nucs-
refined_045-noH-coot-2.pdb, chain A (#4), sequence alignment score = 5405.9  
RMSD between 1292 pruned atom pairs is 1.376 angstroms; (across all 2348
pairs: 4.020)  
  

> matchmaker #!4 to #3/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5nug (1).pdb, chain B (#3) with dynein_local_july27-with-nucs-
refined_045-noH-coot-2.pdb, chain A (#4), sequence alignment score = 5405.9  
RMSD between 1292 pruned atom pairs is 1.376 angstroms; (across all 2348
pairs: 4.020)  
  

> hide #!2 models

> show #!2 models

> hide #!3 models

> distance #4/A:1800@CA #2/D:1800@CA

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
THR 1800 CA and chi_aug1-2-coot-1.pdb #2/D THR 1800 CA: 38.071Å  

> hide #!4 models

> hide #!2 models

> select add #5

1 pseudobond, 2 models selected  

> select subtract #5

Nothing selected  

> hide #!5 models

> show #!5 models

> color #5 #009193 models transparency 0

> distance style #4/A:1800@CA #2/D:1800@CA

> pseudobond #4/A:1800@CA #2/D:1800@CA

Unknown command: pseudobond #4/A:1800@CA #2/D:1800@CA  

> show #!5 target m

> show #!4 models

> select #2/D:1800

14 atoms, 13 bonds, 1 residue, 1 model selected  

> color #4-5 red

> select #2/D:1800

14 atoms, 13 bonds, 1 residue, 1 model selected  

> color #2/D:1800 red

> show #!2 models

> hide #!2 models

> color #4/D:1800 red

> color #4/D:3830 red

> color #4/A:3830 red

> distance style #4/A:3830@CA #2/D:3830@CA

> distance #4/A:3830@CA #2/D:3830@CA

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
SER 3830 CA and chi_aug1-2-coot-1.pdb #2/D SER 3830 CA: 25.210Å  

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide cartoons

> show sel cartoons

> hide #5.1 models

> hide #!5 models

> show #!5 models

> halfbond = Boolean

Unknown command: halfbond = Boolean  

> color = color-spec

Missing or invalid "objects" argument: invalid objects specifier  

> radius = r

Unknown command: radius = r  

> dashes = 3

Unknown command: dashes = 3  

> open /Users/janicereimer/Downloads/pseudobonds.pb

Expected true or false (or 1 or 0)  

> halfbond = Boolean

Unknown command: halfbond = Boolean  

> color = color-spec

Missing or invalid "objects" argument: invalid objects specifier  

> radius = r

Unknown command: radius = r  

> dashes = 3

Unknown command: dashes = 3  

> open /Users/janicereimer/Downloads/pseudobonds.pb

Expected true or false (or 1 or 0)  

> distance #4/A:3830@CA #2/D:3830@CA dashes 3 symbol false decimalPlaces 0

Distance already exists; modify distance properties with 'distance style'  

> close #5

> distance #4/A:3830@CA #2/D:3830@CA dashes 3 symbol false decimalPlaces 0

> distance style decimalPlaces 0

> distance style symbol false

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
SER 3830 CA and chi_aug1-2-coot-1.pdb #2/D SER 3830 CA: 25  

> close #5

> distance #4/A:3830@CA #2/D:3830@CA dashes 0 symbol false decimalPlaces 0

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
SER 3830 CA and chi_aug1-2-coot-1.pdb #2/D SER 3830 CA: 25  

> close #5

> distance #4/A:3830@CA #2/D:3830@CA dashes 0 symbol false decimalPlaces 0
> radius 3

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
SER 3830 CA and chi_aug1-2-coot-1.pdb #2/D SER 3830 CA: 25  

> distance #4/A:3830@CA #2/D:3830@CA dashes 0 symbol false decimalPlaces 0
> radius 2

Distance already exists; modify distance properties with 'distance style'  

> close #5

> distance #4/A:3830@CA #2/D:3830@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
SER 3830 CA and chi_aug1-2-coot-1.pdb #2/D SER 3830 CA: 25  

> close #5

> hide #!2 models

> distance #4/A: 1490 #2/D: 1490 @CA dashes 0 symbol false decimalPlaces 0
> radius 0.6

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #4/A:1490 #2/D:1490 @CA dashes 0 symbol false decimalPlaces 0
> radius 0.6

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #4/A:1660 #2/D:1660@CA dashes 0 symbol false decimalPlaces 0 radius
> 0.23

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
8  

> distance#4/A:1630@CA #2/D:1630@CA dashes 0 symbol false decimalPlaces 0
> radius 0.20

Unknown command: distance#4/A:1630@CA #2/D:1630@CA dashes 0 symbol false
decimalPlaces 0 radius 0.20  

> distance #4/A:1640@CA #2/D:1640@CA dashes 0 symbol false decimalPlaces 0
> radius 0.21

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
VAL 1640 CA and chi_aug1-2-coot-1.pdb #2/D VAL 1640 CA: 43  

> hide #!5 models

> show #!5 models

> distance #4/A:1680@CA #2/D:1680@CA dashes 0 symbol false decimalPlaces 0
> radius 0.21

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
ILE 1680 CA and chi_aug1-2-coot-1.pdb #2/D ILE 1680 CA: 43  

> show #!2 models

> distance #4/A:1640@CA #2/D:1640@CA dashes 0 symbol false decimalPlaces 0
> radius 0.21

Distance already exists; modify distance properties with 'distance style'  

> close #5

> distance #4/A:3830@CA #2/D:3830@CA dashes 0 symbol false decimalPlaces 0
> radius 0.21

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
SER 3830 CA and chi_aug1-2-coot-1.pdb #2/D SER 3830 CA: 25  

> close #5

> distance #4/A:3830@CA #2/D:3830@CA dashes 0 symbol false decimalPlaces 0
> radius 0.21 color green

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #4/A
SER 3830 CA and chi_aug1-2-coot-1.pdb #2/D SER 3830 CA: 25  

> close #5

> distance#4/A:1480@CA #2/D:1480@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1480@CA #2/D:1480@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1490@CA #2/D:1490@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1490@CA #2/D:1490@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1500@CA #2/D:1500@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1500@CA #2/D:1500@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1510@CA #2/D:1510@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1510@CA #2/D:1510@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1520@CA #2/D:1520@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1520@CA #2/D:1520@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1530@CA #2/D:1530@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1530@CA #2/D:1530@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1540@CA #2/D:1540@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1540@CA #2/D:1540@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1550@CA #2/D:1550@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1550@CA #2/D:1550@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1560@CA #2/D:1560@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1560@CA #2/D:1560@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1570@CA #2/D:1570@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1570@CA #2/D:1570@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1580@CA #2/D:1580@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1580@CA #2/D:1580@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1590@CA #2/D:1590@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1590@CA #2/D:1590@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1600@CA #2/D:1600@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1600@CA #2/D:1600@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1610@CA #2/D:1610@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1610@CA #2/D:1610@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1620@CA #2/D:1620@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1620@CA #2/D:1620@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1630@CA #2/D:1630@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1630@CA #2/D:1630@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1640@CA #2/D:1640@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1640@CA #2/D:1640@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1650@CA #2/D:1650@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1650@CA #2/D:1650@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1660@CA #2/D:1660@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1660@CA #2/D:1660@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1670@CA #2/D:1670@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1670@CA #2/D:1670@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1680@CA #2/D:1680@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1680@CA #2/D:1680@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1690@CA #2/D:1690@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1690@CA #2/D:1690@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1700@CA #2/D:1700@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1700@CA #2/D:1700@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1710@CA #2/D:1710@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1710@CA #2/D:1710@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1720@CA #2/D:1720@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1720@CA #2/D:1720@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1730@CA #2/D:1730@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1730@CA #2/D:1730@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1740@CA #2/D:1740@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1740@CA #2/D:1740@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1750@CA #2/D:1750@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1750@CA #2/D:1750@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1760@CA #2/D:1760@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1760@CA #2/D:1760@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1770@CA #2/D:1770@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color purple

Unknown command: distance#4/A:1770@CA #2/D:1770@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color purple  

> distance#4/A:1780@CA #2/D:1780@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1780@CA #2/D:1780@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1790@CA #2/D:1790@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1790@CA #2/D:1790@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1800@CA #2/D:1800@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1800@CA #2/D:1800@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1810@CA #2/D:1810@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1810@CA #2/D:1810@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1820@CA #2/D:1820@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1820@CA #2/D:1820@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1830@CA #2/D:1830@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1830@CA #2/D:1830@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1840@CA #2/D:1840@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1840@CA #2/D:1840@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1850@CA #2/D:1850@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1850@CA #2/D:1850@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1860@CA #2/D:1860@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1860@CA #2/D:1860@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1870@CA #2/D:1870@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1870@CA #2/D:1870@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1880@CA #2/D:1880@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1880@CA #2/D:1880@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1890@CA #2/D:1890@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1890@CA #2/D:1890@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1900@CA #2/D:1900@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1900@CA #2/D:1900@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1910@CA #2/D:1910@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1910@CA #2/D:1910@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1920@CA #2/D:1920@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1920@CA #2/D:1920@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1930@CA #2/D:1930@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1930@CA #2/D:1930@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1940@CA #2/D:1940@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1940@CA #2/D:1940@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1950@CA #2/D:1950@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1950@CA #2/D:1950@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1960@CA #2/D:1960@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1960@CA #2/D:1960@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

> distance#4/A:1970@CA #2/D:1970@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color midnight blue

Unknown command: distance#4/A:1970@CA #2/D:1970@CA dashes 0 symbol false
decimalPlaces 0 radius 0.5 color midnight blue  

[much of the log deleted to fit within ticket length limits]

> distance #3/A:3480@CA #2/A:3480@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 3480 CA and chi_aug1-2-coot-2.pdb #2/A GLU 3480 CA: 13  

> distance #3/A:3485@CA #2/A:3485@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 3485 CA and chi_aug1-2-coot-2.pdb #2/A GLU 3485 CA: 13  

> distance #3/A:3490@CA #2/A:3490@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLY 3490 CA and chi_aug1-2-coot-2.pdb #2/A GLY 3490 CA: 11  

> distance #3/A:3495@CA #2/A:3495@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PHE 3495 CA and chi_aug1-2-coot-2.pdb #2/A PHE 3495 CA: 10  

> distance #3/A:3500@CA #2/A:3500@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASP 3500 CA and chi_aug1-2-coot-2.pdb #2/A ASP 3500 CA: 11  

> distance #3/A:3505@CA #2/A:3505@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ILE 3505 CA and chi_aug1-2-coot-2.pdb #2/A ILE 3505 CA: 12  

> distance #3/A:3510@CA #2/A:3510@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ARG 3510 CA and chi_aug1-2-coot-2.pdb #2/A ARG 3510 CA: 12  

> distance #3/A:3515@CA #2/A:3515@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3515 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3515 CA: 11  

> distance #3/A:3520@CA #2/A:3520@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
THR 3520 CA and chi_aug1-2-coot-2.pdb #2/A THR 3520 CA: 9  

> distance #3/A:3525@CA #2/A:3525@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ILE 3525 CA and chi_aug1-2-coot-2.pdb #2/A ILE 3525 CA: 9  

> distance #3/A:3530@CA #2/A:3530@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PHE 3530 CA and chi_aug1-2-coot-2.pdb #2/A PHE 3530 CA: 8  

> distance #3/A:3535@CA #2/A:3535@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
THR 3535 CA and chi_aug1-2-coot-2.pdb #2/A THR 3535 CA: 7  

> distance #3/A:3540@CA #2/A:3540@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 3540 CA and chi_aug1-2-coot-2.pdb #2/A GLU 3540 CA: 7  

> distance #3/A:3545@CA #2/A:3545@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ARG 3545 CA and chi_aug1-2-coot-2.pdb #2/A ARG 3545 CA: 7  

> distance #3/A:3550@CA #2/A:3550@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LYS 3550 CA and chi_aug1-2-coot-2.pdb #2/A LYS 3550 CA: 7  

> distance #3/A:3555@CA #2/A:3555@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
TYR 3555 CA and chi_aug1-2-coot-2.pdb #2/A TYR 3555 CA: 7  

> distance #3/A:3560@CA #2/A:3560@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LYS 3560 CA and chi_aug1-2-coot-2.pdb #2/A LYS 3560 CA: 7  

> distance #3/A:3565@CA #2/A:3565@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ARG 3565 CA and chi_aug1-2-coot-2.pdb #2/A ARG 3565 CA: 7  

> distance #3/A:3570@CA #2/A:3570@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3570 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3570 CA: 7  

> distance #3/A:3575@CA #2/A:3575@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLY 3575 CA and chi_aug1-2-coot-2.pdb #2/A GLY 3575 CA: 7  

> distance #3/A:3580@CA #2/A:3580@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASN 3580 CA and chi_aug1-2-coot-2.pdb #2/A ASN 3580 CA: 7  

> distance #3/A:3585@CA #2/A:3585@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
VAL 3585 CA and chi_aug1-2-coot-2.pdb #2/A VAL 3585 CA: 7  

> distance #3/A:3590@CA #2/A:3590@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3590 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3590 CA: 7  

> distance #3/A:3595@CA #2/A:3595@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
MET 3595 CA and chi_aug1-2-coot-2.pdb #2/A MET 3595 CA: 7  

> distance #3/A:3600@CA #2/A:3600@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LYS 3600 CA and chi_aug1-2-coot-2.pdb #2/A LYS 3600 CA: 7  

> distance #3/A:3605@CA #2/A:3605@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 3605 CA and chi_aug1-2-coot-2.pdb #2/A GLU 3605 CA: 7  

> distance #3/A:3610@CA #2/A:3610@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLN 3610 CA and chi_aug1-2-coot-2.pdb #2/A GLN 3610 CA: 7  

> distance #3/A:3615@CA #2/A:3615@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
VAL 3615 CA and chi_aug1-2-coot-2.pdb #2/A VAL 3615 CA: 8  

> distance #3/A:3620@CA #2/A:3620@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ILE 3620 CA and chi_aug1-2-coot-2.pdb #2/A ILE 3620 CA: 8  

> distance #3/A:3625@CA #2/A:3625@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3625 CA and chi_aug1-2-coot-2.pdb #2/A SER 3625 CA: 9  

> distance #3/A:3630@CA #2/A:3630@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3630 CA and chi_aug1-2-coot-2.pdb #2/A SER 3630 CA: 10  

> distance #3/A:3635@CA #2/A:3635@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PHE 3635 CA and chi_aug1-2-coot-2.pdb #2/A PHE 3635 CA: 10  

> distance #3/A:3640@CA #2/A:3640@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
TRP 3640 CA and chi_aug1-2-coot-2.pdb #2/A TRP 3640 CA: 11  

> distance #3/A:3645@CA #2/A:3645@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3645 CA and chi_aug1-2-coot-2.pdb #2/A SER 3645 CA: 10  

> distance #3/A:3650@CA #2/A:3650@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3650 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3650 CA: 8  

> distance #3/A:3655@CA #2/A:3655@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ARG 3655 CA and chi_aug1-2-coot-2.pdb #2/A ARG 3655 CA: 8  

> distance #3/A:3660@CA #2/A:3660@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:3665@CA #2/A:3665@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:3670@CA #2/A:3670@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ARG 3670 CA and chi_aug1-2-coot-2.pdb #2/A ARG 3670 CA: 8  

> distance #3/A:3675@CA #2/A:3675@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3675 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3675 CA: 8  

> distance #3/A:3680@CA #2/A:3680@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLN 3680 CA and chi_aug1-2-coot-2.pdb #2/A GLN 3680 CA: 8  

> distance #3/A:3685@CA #2/A:3685@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLN 3685 CA and chi_aug1-2-coot-2.pdb #2/A GLN 3685 CA: 9  

> distance #3/A:3690@CA #2/A:3690@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3690 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3690 CA: 10  

> distance #3/A:3695@CA #2/A:3695@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LYS 3695 CA and chi_aug1-2-coot-2.pdb #2/A LYS 3695 CA: 10  

> distance #3/A:3700@CA #2/A:3700@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
MET 3700 CA and chi_aug1-2-coot-2.pdb #2/A MET 3700 CA: 10  

> distance #3/A:3705@CA #2/A:3705@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3705 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3705 CA: 10  

> distance #3/A:3710@CA #2/A:3710@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ILE 3710 CA and chi_aug1-2-coot-2.pdb #2/A ILE 3710 CA: 9  

> distance #3/A:3715@CA #2/A:3715@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
TYR 3715 CA and chi_aug1-2-coot-2.pdb #2/A TYR 3715 CA: 10  

> distance #3/A:3720@CA #2/A:3720@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3720 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3720 CA: 11  

> distance #3/A:3725@CA #2/A:3725@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
VAL 3725 CA and chi_aug1-2-coot-2.pdb #2/A VAL 3725 CA: 12  

> distance #3/A:3730@CA #2/A:3730@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3730 CA and chi_aug1-2-coot-2.pdb #2/A SER 3730 CA: 13  

> distance #3/A:3735@CA #2/A:3735@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LYS 3735 CA and chi_aug1-2-coot-2.pdb #2/A LYS 3735 CA: 11  

> distance #3/A:3740@CA #2/A:3740@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:3745@CA #2/A:3745@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ARG 3745 CA and chi_aug1-2-coot-2.pdb #2/A ARG 3745 CA: 11  

> distance #3/A:3750@CA #2/A:3750@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
TYR 3750 CA and chi_aug1-2-coot-2.pdb #2/A TYR 3750 CA: 11  

> distance #3/A:3755@CA #2/A:3755@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3755 CA and chi_aug1-2-coot-2.pdb #2/A SER 3755 CA: 11  

> distance #3/A:3760@CA #2/A:3760@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3760 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3760 CA: 10  

> distance #3/A:3765@CA #2/A:3765@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASN 3765 CA and chi_aug1-2-coot-2.pdb #2/A ASN 3765 CA: 9  

> distance #3/A:3770@CA #2/A:3770@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color chocolate

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASP 3770 CA and chi_aug1-2-coot-2.pdb #2/A ASP 3770 CA: 9  

> distance #3/A:3775@CA #2/A:3775@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ALA 3775 CA and chi_aug1-2-coot-2.pdb #2/A ALA 3775 CA: 9  

> distance #3/A:3780@CA #2/A:3780@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASN 3780 CA and chi_aug1-2-coot-2.pdb #2/A ASN 3780 CA: 8  

> distance #3/A:3785@CA #2/A:3785@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
TYR 3785 CA and chi_aug1-2-coot-2.pdb #2/A TYR 3785 CA: 10  

> distance #3/A:3790@CA #2/A:3790@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3790 CA and chi_aug1-2-coot-2.pdb #2/A SER 3790 CA: 11  

> distance #3/A:3795@CA #2/A:3795@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASP 3795 CA and chi_aug1-2-coot-2.pdb #2/A ASP 3795 CA: 11  

> distance #3/A:3800@CA #2/A:3800@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3800 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3800 CA: 10  

> distance #3/A:3805@CA #2/A:3805@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LYS 3805 CA and chi_aug1-2-coot-2.pdb #2/A LYS 3805 CA: 9  

> distance #3/A:3810@CA #2/A:3810@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3810 CA and chi_aug1-2-coot-2.pdb #2/A SER 3810 CA: 10  

> distance #3/A:3815@CA #2/A:3815@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PRO 3815 CA and chi_aug1-2-coot-2.pdb #2/A PRO 3815 CA: 12  

> distance #3/A:3820@CA #2/A:3820@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 3820 CA and chi_aug1-2-coot-2.pdb #2/A GLU 3820 CA: 12  

> distance #3/A:3825@CA #2/A:3825@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ALA 3825 CA and chi_aug1-2-coot-2.pdb #2/A ALA 3825 CA: 11  

> distance #3/A:3830@CA #2/A:3830@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3830 CA and chi_aug1-2-coot-2.pdb #2/A SER 3830 CA: 11  

> distance #3/A:3835@CA #2/A:3835@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 3835 CA and chi_aug1-2-coot-2.pdb #2/A GLU 3835 CA: 10  

> distance #3/A:3840@CA #2/A:3840@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3840 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3840 CA: 10  

> distance #3/A:3845@CA #2/A:3845@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLN 3845 CA and chi_aug1-2-coot-2.pdb #2/A GLN 3845 CA: 12  

> distance #3/A:3850@CA #2/A:3850@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
TRP 3850 CA and chi_aug1-2-coot-2.pdb #2/A TRP 3850 CA: 12  

> distance #3/A:3855@CA #2/A:3855@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3855 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3855 CA: 11  

> distance #3/A:3860@CA #2/A:3860@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 3860 CA and chi_aug1-2-coot-2.pdb #2/A GLU 3860 CA: 10  

> distance #3/A:3865@CA #2/A:3865@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ALA 3865 CA and chi_aug1-2-coot-2.pdb #2/A ALA 3865 CA: 9  

> distance #3/A:3870@CA #2/A:3870@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LYS 3870 CA and chi_aug1-2-coot-2.pdb #2/A LYS 3870 CA: 9  

> distance #3/A:3875@CA #2/A:3875@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
MET 3875 CA and chi_aug1-2-coot-2.pdb #2/A MET 3875 CA: 11  

> distance #3/A:3880@CA #2/A:3880@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
THR 3880 CA and chi_aug1-2-coot-2.pdb #2/A THR 3880 CA: 12  

> distance #3/A:3885@CA #2/A:3885@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PRO 3885 CA and chi_aug1-2-coot-2.pdb #2/A PRO 3885 CA: 11  

> distance #3/A:3890@CA #2/A:3890@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLN 3890 CA and chi_aug1-2-coot-2.pdb #2/A GLN 3890 CA: 10  

> distance #3/A:3895@CA #2/A:3895@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
VAL 3895 CA and chi_aug1-2-coot-2.pdb #2/A VAL 3895 CA: 10  

> distance #3/A:3900@CA #2/A:3900@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ILE 3900 CA and chi_aug1-2-coot-2.pdb #2/A ILE 3900 CA: 10  

> distance #3/A:3905@CA #2/A:3905@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASP 3905 CA and chi_aug1-2-coot-2.pdb #2/A ASP 3905 CA: 9  

> distance #3/A:3910@CA #2/A:3910@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3910 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3910 CA: 9  

> distance #3/A:3915@CA #2/A:3915@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:3920@CA #2/A:3920@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:3925@CA #2/A:3925@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3925 CA and chi_aug1-2-coot-2.pdb #2/A SER 3925 CA: 9  

> distance #3/A:3930@CA #2/A:3930@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PHE 3930 CA and chi_aug1-2-coot-2.pdb #2/A PHE 3930 CA: 9  

> distance #3/A:3935@CA #2/A:3935@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PHE 3935 CA and chi_aug1-2-coot-2.pdb #2/A PHE 3935 CA: 11  

> distance #3/A:3940@CA #2/A:3940@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
THR 3940 CA and chi_aug1-2-coot-2.pdb #2/A THR 3940 CA: 11  

> distance #3/A:3945@CA #2/A:3945@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 3945 CA and chi_aug1-2-coot-2.pdb #2/A LEU 3945 CA: 12  

> distance #3/A:3950@CA #2/A:3950@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PHE 3950 CA and chi_aug1-2-coot-2.pdb #2/A PHE 3950 CA: 13  

> distance #3/A:3955@CA #2/A:3955@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
TYR 3955 CA and chi_aug1-2-coot-2.pdb #2/A TYR 3955 CA: 12  

> distance #3/A:3960@CA #2/A:3960@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASP 3960 CA and chi_aug1-2-coot-2.pdb #2/A ASP 3960 CA: 11  

> distance #3/A:3965@CA #2/A:3965@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 3965 CA and chi_aug1-2-coot-2.pdb #2/A SER 3965 CA: 10  

> distance #3/A:3970@CA #2/A:3970@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASN 3970 CA and chi_aug1-2-coot-2.pdb #2/A ASN 3970 CA: 10  

> distance #3/A:3975@CA #2/A:3975@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASN 3975 CA and chi_aug1-2-coot-2.pdb #2/A ASN 3975 CA: 10  

> distance #3/A:3980@CA #2/A:3980@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ILE 3980 CA and chi_aug1-2-coot-2.pdb #2/A ILE 3980 CA: 10  

> distance #3/A:3985@CA #2/A:3985@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
VAL 3985 CA and chi_aug1-2-coot-2.pdb #2/A VAL 3985 CA: 11  

> distance #3/A:3990@CA #2/A:3990@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ALA 3990 CA and chi_aug1-2-coot-2.pdb #2/A ALA 3990 CA: 12  

> distance #3/A:3995@CA #2/A:3995@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLY 3995 CA and chi_aug1-2-coot-2.pdb #2/A GLY 3995 CA: 12  

> distance #3/A:4000@CA #2/A:4000@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 4000 CA and chi_aug1-2-coot-2.pdb #2/A GLU 4000 CA: 13  

> distance #3/A:4005@CA #2/A:4005@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 4005 CA and chi_aug1-2-coot-2.pdb #2/A GLU 4005 CA: 13  

> distance #3/A:4010@CA #2/A:4010@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 4010 CA and chi_aug1-2-coot-2.pdb #2/A LEU 4010 CA: 12  

> distance #3/A:4015@CA #2/A:4015@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PHE 4015 CA and chi_aug1-2-coot-2.pdb #2/A PHE 4015 CA: 11  

> distance #3/A:4020@CA #2/A:4020@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ASN 4020 CA and chi_aug1-2-coot-2.pdb #2/A ASN 4020 CA: 10  

> distance #3/A:4025@CA #2/A:4025@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PRO 4025 CA and chi_aug1-2-coot-2.pdb #2/A PRO 4025 CA: 11  

> distance #3/A:4030@CA #2/A:4030@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PRO 4030 CA and chi_aug1-2-coot-2.pdb #2/A PRO 4030 CA: 9  

> distance #3/A:4035@CA #2/A:4035@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLN 4035 CA and chi_aug1-2-coot-2.pdb #2/A GLN 4035 CA: 8  

> distance #3/A:4040@CA #2/A:4040@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 4040 CA and chi_aug1-2-coot-2.pdb #2/A GLU 4040 CA: 8  

> distance #3/A:4045@CA #2/A:4045@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 4045 CA and chi_aug1-2-coot-2.pdb #2/A LEU 4045 CA: 9  

> distance #3/A:4050@CA #2/A:4050@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 4050 CA and chi_aug1-2-coot-2.pdb #2/A SER 4050 CA: 9  

> distance #3/A:4055@CA #2/A:4055@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
PRO 4055 CA and chi_aug1-2-coot-2.pdb #2/A PRO 4055 CA: 10  

> distance #3/A:4060@CA #2/A:4060@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
SER 4060 CA and chi_aug1-2-coot-2.pdb #2/A SER 4060 CA: 11  

> distance #3/A:4065@CA #2/A:4065@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
LEU 4065 CA and chi_aug1-2-coot-2.pdb #2/A LEU 4065 CA: 12  

> distance #3/A:4070@CA #2/A:4070@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ILE 4070 CA and chi_aug1-2-coot-2.pdb #2/A ILE 4070 CA: 12  

> distance #3/A:4075@CA #2/A:4075@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
ARG 4075 CA and chi_aug1-2-coot-2.pdb #2/A ARG 4075 CA: 12  

> distance #3/A:4080@CA #2/A:4080@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLU 4080 CA and chi_aug1-2-coot-2.pdb #2/A GLU 4080 CA: 12  

> distance #3/A:4085@CA #2/A:4085@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
THR 4085 CA and chi_aug1-2-coot-2.pdb #2/A THR 4085 CA: 11  

> distance #3/A:4090@CA #2/A:4090@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Distance between dynein_local_july27-with-nucs-refined_045-noH-coot-2.pdb #3/A
GLN 4090 CA and chi_aug1-2-coot-2.pdb #2/A GLN 4090 CA: 11  

> distance #3/A:4095@CA #2/A:4095@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:4100@CA #2/A:4100@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:4105@CA #2/A:4105@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:4110@CA #2/A:4110@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:4115@CA #2/A:4115@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> distance #3/A:4120@CA #2/A:4120@CA dashes 0 symbol false decimalPlaces 0
> radius 0.5 color dark red

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0  

> hide #5.1 models

> save
> /Users/janicereimer/Dropbox/Chi_Lis1/Figures/Figure2_files/2B_phi_to_chi-
> centered.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 543, in include_state  
return bool(self.group_map)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 387, in __getattr__  
func = self.__getitem__(name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  

Populating font family aliases took 303 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 543, in include_state  
return bool(self.group_map)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 387, in __getattr__  
func = self.__getitem__(name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  
AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  

> save
> /Users/janicereimer/Dropbox/Chi_Lis1/Figures/Figure2_files/2B_phi_to_chi-
> centered2.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 543, in include_state  
return bool(self.group_map)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 387, in __getattr__  
func = self.__getitem__(name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  
AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.4.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
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 543, in include_state  
return bool(self.group_map)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 387, in __getattr__  
func = self.__getitem__(name)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  
AttributeError: dlsym(0x20e570b40, set_pbgroup_py_instance): symbol not found  
  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.54
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
      OS Loader Version: 540.120.3~6

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 8 days 9:03

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501U-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DP:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 100.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Sessions
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Session save: function 'set_pbgroup_py_instance' not found

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Janice,

Thanks for reporting this problem. It was fixed about a month and a half ago and the fix is in the daily build. So if you get that then you won't run into this problem anymore. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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