Opened 3 years ago

Last modified 3 years ago

#8460 assigned defect

self._current_reference is None

Reported by: mille153@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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
Loading a PAE file

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

> open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs

Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33,
shown at level 0.0974, step 1, values float32  
Log from Tue Feb 7 14:18:19 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs

Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33,
shown at level 0.0974, step 1, values float32  
Log from Thu Feb 2 16:14:31 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:user

> open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold-
> model-5-1.pdb

Chain information for fnv-m-alphafold-model-5-1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/andrewmiller/Documents/FNV-modeling/FNV-M-model-5-chainD-
> edit.pdb

Chain information for FNV-M-model-5-chainD-edit.pdb #2  
---  
Chain | Description  
D | No description available  
  

> open /Users/andrewmiller/Documents/FNV-modeling/FNV-M-model-5-chainF-
> edit.pdb

Chain information for FNV-M-model-5-chainF-edit.pdb #3  
---  
Chain | Description  
F | No description available  
  

> open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold-
> model-5-1.pdb

Chain information for fnv-m-alphafold-model-5-1.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> show #1 models

> open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold-
> model-5-1.pdb

Chain information for fnv-m-alphafold-model-5-1.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #4 models

> hide #5 models

> show #5 models

> show #4 models

> show #1 models

> matchmaker #5 to #2

Parameters  
---  
Chain pairing | bb  
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 FNV-M-model-5-chainD-edit.pdb, chain D (#2) with fnv-m-alphafold-
model-5-1.pdb, chain A (#5), sequence alignment score = 276.1  
RMSD between 49 pruned atom pairs is 0.948 angstroms; (across all 58 pairs:
2.540)  
  

> matchmaker #4 to #3

Parameters  
---  
Chain pairing | bb  
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 FNV-M-model-5-chainF-edit.pdb, chain F (#3) with fnv-m-alphafold-
model-5-1.pdb, chain A (#4), sequence alignment score = 276.1  
RMSD between 49 pruned atom pairs is 0.948 angstroms; (across all 58 pairs:
2.540)  
  

> hide #4 models

> show #4 models

Populating font family aliases took 168 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

> save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainF-
> edit.pdb models #4

> hide #5 models

> show #5 models

> save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainD-
> edit.pdb models #5

> save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainB-
> edit.pdb models #1

> close session

> open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4

Opened test-fnv-asu_box.ccp4 as #1, grid size 81,145,67, pixel 1.33, shown at
level 0.168, step 1, values float32  

> set bgColor white

> set bgColor #ffffff00

> volume #1 level 0.107

> open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best-
> model-edit.pdb

Chain information for FNV-E-prediction-1-best-model-edit.pdb #2  
---  
Chain | Description  
A | No description available  
  

> transparency 50

> open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best-
> model-edit.pdb

Chain information for FNV-E-prediction-1-best-model-edit.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best-
> model-edit.pdb

Chain information for FNV-E-prediction-1-best-model-edit.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select add #4

7449 atoms, 7530 bonds, 493 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-20.268,0,1,0,-48.587,0,0,1,13.227

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.99857,0.049338,0.020729,772.69,-0.032585,-0.86781,0.49583,519.1,0.042452,0.49445,0.86817,-150.72

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.99857,0.049338,0.020729,789.19,-0.032585,-0.86781,0.49583,500.69,0.042452,0.49445,0.86817,-146.12

> view matrix models
> #4,-0.99857,0.049338,0.020729,790.53,-0.032585,-0.86781,0.49583,500.53,0.042452,0.49445,0.86817,-145.92

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.99885,0.040425,0.025861,791.66,-0.022372,-0.86901,0.4943,497.76,0.042455,0.49315,0.86891,-145.77

> ui mousemode right "translate selected models"

> ui tool show "Fit in Map"

> fitmap #4 inMap #1

Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#4) to map test-fnv-
asu_box.ccp4 (#1) using 7449 atoms  
average map value = 0.1097, steps = 128  
shifted from previous position = 9.03  
rotated from previous position = 15.1 degrees  
atoms outside contour = 3535, contour level = 0.107  
  
Position of FNV-E-prediction-1-best-model-edit.pdb (#4) relative to test-fnv-
asu_box.ccp4 (#1) coordinates:  
Matrix rotation and translation  
-0.97725858 0.02825152 0.21016072 679.12240517  
0.04060965 -0.94780665 0.31624897 609.72599973  
0.20812624 0.31759157 0.92510489 -174.14668121  
Axis 0.10658756 0.16151476 0.98109738  
Axis point 348.04241714 320.28749895 0.00000000  
Rotation angle (degrees) 179.63914225  
Shift along axis 0.01089425  
  

> select subtract #4

Nothing selected  

> select add #3

7449 atoms, 7530 bonds, 493 residues, 1 model selected  

> view matrix models #3,1,0,0,32.528,0,1,0,-10.989,0,0,1,4.6657

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.9561,-0.073497,-0.28369,1044.2,0.075903,-0.99711,0.0025182,863.07,-0.28305,-0.019125,0.95891,154.94

> view matrix models
> #3,-0.94178,-0.08722,-0.32471,1068.9,0.063398,-0.99451,0.083256,819.18,-0.33019,0.057824,0.94214,149.46

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.94178,-0.08722,-0.32471,1068,0.063398,-0.99451,0.083256,803.24,-0.33019,0.057824,0.94214,149.27

> fitmap #3 inMap #1

Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#3) to map test-fnv-
asu_box.ccp4 (#1) using 7449 atoms  
average map value = 0.1057, steps = 224  
shifted from previous position = 3.16  
rotated from previous position = 55.2 degrees  
atoms outside contour = 3805, contour level = 0.107  
  
Position of FNV-E-prediction-1-best-model-edit.pdb (#3) relative to test-fnv-
asu_box.ccp4 (#1) coordinates:  
Matrix rotation and translation  
-0.91036793 0.12790971 0.39353442 524.69773237  
0.14183002 -0.79696794 0.58713401 377.91727979  
0.38873446 0.59032296 0.70739262 -250.71847076  
Axis 0.21166597 0.31859580 0.92395575  
Axis point 290.29657732 233.25421562 -0.00000000  
Rotation angle (degrees) 179.56838716  
Shift along axis -0.18925892  
  

> view matrix models
> #3,-0.91037,0.12791,0.39353,524.11,0.14183,-0.79697,0.58713,376.06,0.38873,0.59032,0.70739,-250.55

> view matrix models
> #3,-0.91037,0.12791,0.39353,524.12,0.14183,-0.79697,0.58713,376.12,0.38873,0.59032,0.70739,-250.55

> fitmap #3 inMap #1

Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#3) to map test-fnv-
asu_box.ccp4 (#1) using 7449 atoms  
average map value = 0.1057, steps = 52  
shifted from previous position = 1.91  
rotated from previous position = 0.0252 degrees  
atoms outside contour = 3806, contour level = 0.107  
  
Position of FNV-E-prediction-1-best-model-edit.pdb (#3) relative to test-fnv-
asu_box.ccp4 (#1) coordinates:  
Matrix rotation and translation  
-0.91035553 0.12831748 0.39343034 524.59477571  
0.14143086 -0.79699351 0.58719559 378.06830941  
0.38890889 0.59019994 0.70739939 -250.74625657  
Axis 0.21168422 0.31857800 0.92395771  
Axis point 290.29507266 233.26980806 0.00000000  
Rotation angle (degrees) 179.59340820  
Shift along axis -0.18625781  
  

> ui mousemode right select

> select clear

> view orient

> save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainA-
> edit.pdb models #4 relModel #1

> view orient

> save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainC-
> edit.pdb models #2 relModel #1

> save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainE-
> edit.pdb models #3 relModel #1

> close session

> set bgColor white

> open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4

Opened test-fnv-asu_box.ccp4 as #1, grid size 81,145,67, pixel 1.33, shown at
level 0.168, step 1, values float32  

> open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.pdb

Chain information for 020223-FNV-alphafold-asu.pdb #2  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
  

> hide atoms

> style stick

Changed 25200 atom styles  

> style stick

Changed 25200 atom styles  

> show atoms

> show cartoons

> hide atoms

> volume #1 level 0.1108

> transparency 50

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 020223-FNV-alphafold-asu.pdb  
---  
Chain | Description  
2.2/A 2.2/C 2.2/E | No description available  
2.2/B 2.2/D 2.2/F | No description available  
  
ISOLDE: created disulfide bonds between the following residues:  
E92-E116; A92-A116; A74-A105; C3-C30; E3-E30; C60-C121; A3-A30; A300-A330;
C74-C105; C300-C330; A182-A283; C92-C116; E60-E121; E300-E330; E74-E105;
C182-C283; A60-A121; E182-E283  

> clipper associate #1 toModel #2

Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33,
shown at step 1, values float32  

> volume #2.1.1.1 level 0.09739

> select add #2.2

25200 atoms, 25473 bonds, 1653 residues, 6 models selected  

> addh

Summary of feedback from adding hydrogens to 020223-FNV-alphafold-asu.pdb #2.2  
---  
notes | No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain
A; guessing termini instead  
No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain B;
guessing termini instead  
No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain C;
guessing termini instead  
No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain D;
guessing termini instead  
No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain E;
guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ALA 1, /C ALA 1, /E ALA 1  
Chain-initial residues that are not actual N termini: /B LYS 18, /D LYS 18, /F
LYS 18  
Chain-final residues that are actual C termini: /A ALA 493, /C ALA 493, /E ALA
493  
Chain-final residues that are not actual C termini: /B SER 75, /D SER 75, /F
SER 75  
1432 hydrogen bonds  
/B SER 75 is not terminus, removing H atom from 'C'  
/D SER 75 is not terminus, removing H atom from 'C'  
/F SER 75 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> ui tool show "Ramachandran Plot"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 287, in process  
func(*args, **kwargs)  
File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize  
c.draw()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 436, in draw  
self.figure.draw(self.renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 73, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 50, in draw_wrapper  
return draw(artist, renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 2796, in draw  
artists = self._get_draw_artists(renderer)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 238, in _get_draw_artists  
ax.apply_aspect()  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1890, in apply_aspect  
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect  
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")  
ValueError: 'box_aspect' and 'fig_aspect' must be positive  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs

[Repeated 1 time(s)]

——— End of log from Thu Feb 2 16:14:31 2023 ———

opened ChimeraX session  

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs

——— End of log from Tue Feb 7 14:18:19 2023 ———

opened ChimeraX session  

> close session

> open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.pdb

Chain information for 020223-FNV-alphafold-asu.pdb #1  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
  

> style stick

Changed 25011 atom styles  

> show cartoons

> hide atoms

> open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4

Opened test-fnv-asu_box.ccp4 as #2, grid size 81,145,67, pixel 1.33, shown at
level 0.168, step 1, values float32  

> volume #2 level 0.1034

> transparency 50

> isolde start

> set selectionWidth 4

Populating font family aliases took 156 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 020223-FNV-alphafold-asu.pdb  
---  
Chain | Description  
1.2/A 1.2/C 1.2/E | No description available  
1.2/B 1.2/D 1.2/F | No description available  
  
ISOLDE: created disulfide bonds between the following residues:  
A60-A121; A74-A105; C74-C105; C92-C116; A3-A30; C300-C330; C182-C283;
E74-E105; E182-E283; E92-E116; A300-A330; C3-C30; E3-E30; E300-E330; A92-A116;
C60-C121; A182-A283; E60-E121  

> clipper associate #2 toModel #1

Opened test-fnv-asu_box.ccp4 as #1.1.1.1, grid size 81,145,67, pixel 1.33,
shown at step 1, values float32  

> volume #1.1.1.1 level 0.1058

> ui tool show "Ramachandran Plot"

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> volume #1.1.1.1 style surface

> transparency 50

> select clear

> show cartoons

[Repeated 1 time(s)]

> hide atoms

> ui tool show "Ramachandran Plot"

> volume #1.1.1.1 level 0.09391

> show sel atoms

> select clear

> select add #1.2

25011 atoms, 25278 bonds, 1644 residues, 11 models selected  

> show sel atoms

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> volume #1.1.1.1 level 0.08533

> select clear

[Repeated 1 time(s)]

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> select clear

[Repeated 3 time(s)]

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> select #1.2/A:201

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

> isolde sim start sel

ISOLDE: started sim  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> isolde sim start sel

ISOLDE: started sim  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

[Repeated 1 time(s)]

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> select clear

[Repeated 1 time(s)]

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> select clear

[Repeated 2 time(s)]

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> select clear

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
> asu-1.cxs

Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb  

> isolde cisflip #1.2/A:329

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde cisflip #1.2/E:329

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde cisflip #1.2/C:329

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde cisflip #1.2/C:329

Performing cis<\-->trans flip for 1 residues  
ISOLDE: started sim  

> isolde sim stop discardTo start

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> view orient

> select add #1.2

25011 atoms, 25278 bonds, 1644 residues, 11 models selected  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  
ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> ui mousemode right "isolde tug residue"

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

> volume #1.1.1.1 level 0.09105

> volume #1.1.1.1 level 0.09534

Traceback (most recent call last):  
File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343, in
_load_pae_from_file  
run(self.session,f'alphafold pae #{self._current_reference.id_string} file
"{selected_file}" plot false')  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343, in
_load_pae_from_file  
run(self.session,f'alphafold pae #{self._current_reference.id_string} file
"{selected_file}" plot false')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343, in
_load_pae_from_file  
run(self.session,f'alphafold pae #{self._current_reference.id_string} file
"{selected_file}" plot false')  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
AttributeError: 'NoneType' object has no attribute 'id_string'  
  
File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343, in
_load_pae_from_file  
run(self.session,f'alphafold pae #{self._current_reference.id_string} file
"{selected_file}" plot false')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

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: MacBookPro18,1
      Model Number: MK193LL/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 4 hours, 25 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 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-Clipper: 0.18.0
    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-ISOLDE: 1.4
    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 (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → self._current_reference is None

Reported by Andrew Miller

in reply to:  2 ; comment:2 by mille153@…, 3 years ago 

Hi
I forgot to add a reference model, sorry about that
Andy
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, February 8, 2023 2:18 PM
To: Miller, Andrew S <mille153@purdue.edu>
Subject: [ChimeraX] #8460: ChimeraX bug report submission

---- External Email: Use caution with attachments, links, or sharing data ----


#8460: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  mille153@…  |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
 {{{
 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
 Loading a PAE file

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

 > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 asu.cxs

 Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33,
 shown at level 0.0974, step 1, values float32
 Log from Tue Feb 7 14:18:19 2023UCSF ChimeraX version: 1.4 (2022-06-03)
 © 2016-2022 Regents of the University of California. All rights reserved.

 > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 asu.cxs

 Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33,
 shown at level 0.0974, step 1, values float32
 Log from Thu Feb 2 16:14:31 2023UCSF ChimeraX version: 1.4 (2022-06-03)
 © 2016-2022 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > help help:user

 > open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold-
 > model-5-1.pdb

 Chain information for fnv-m-alphafold-model-5-1.pdb #1
 ---
 Chain | Description
 A | No description available


 > open /Users/andrewmiller/Documents/FNV-modeling/FNV-M-model-5-chainD-
 > edit.pdb

 Chain information for FNV-M-model-5-chainD-edit.pdb #2
 ---
 Chain | Description
 D | No description available


 > open /Users/andrewmiller/Documents/FNV-modeling/FNV-M-model-5-chainF-
 > edit.pdb

 Chain information for FNV-M-model-5-chainF-edit.pdb #3
 ---
 Chain | Description
 F | No description available


 > open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold-
 > model-5-1.pdb

 Chain information for fnv-m-alphafold-model-5-1.pdb #4
 ---
 Chain | Description
 A | No description available


 > hide #1 models

 > show #1 models

 > open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold-
 > model-5-1.pdb

 Chain information for fnv-m-alphafold-model-5-1.pdb #5
 ---
 Chain | Description
 A | No description available


 > hide #1 models

 > hide #4 models

 > hide #5 models

 > show #5 models

 > show #4 models

 > show #1 models

 > matchmaker #5 to #2

 Parameters
 ---
 Chain pairing | bb
 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 FNV-M-model-5-chainD-edit.pdb, chain D (#2) with
 fnv-m-alphafold-
 model-5-1.pdb, chain A (#5), sequence alignment score = 276.1
 RMSD between 49 pruned atom pairs is 0.948 angstroms; (across all 58
 pairs:
 2.540)


 > matchmaker #4 to #3

 Parameters
 ---
 Chain pairing | bb
 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 FNV-M-model-5-chainF-edit.pdb, chain F (#3) with
 fnv-m-alphafold-
 model-5-1.pdb, chain A (#4), sequence alignment score = 276.1
 RMSD between 49 pruned atom pairs is 0.948 angstroms; (across all 58
 pairs:
 2.540)


 > hide #4 models

 > show #4 models

 Populating font family aliases took 168 ms. Replace uses of missing font
 family ".AppleSystemUIFont" with one that exists to avoid this cost.

 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainF-
 > edit.pdb models #4

 > hide #5 models

 > show #5 models

 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainD-
 > edit.pdb models #5

 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainB-
 > edit.pdb models #1

 > close session

 > open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4

 Opened test-fnv-asu_box.ccp4 as #1, grid size 81,145,67, pixel 1.33, shown
 at
 level 0.168, step 1, values float32

 > set bgColor white

 > set bgColor #ffffff00

 > volume #1 level 0.107

 > open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best-
 > model-edit.pdb

 Chain information for FNV-E-prediction-1-best-model-edit.pdb #2
 ---
 Chain | Description
 A | No description available


 > transparency 50

 > open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best-
 > model-edit.pdb

 Chain information for FNV-E-prediction-1-best-model-edit.pdb #3
 ---
 Chain | Description
 A | No description available


 > open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best-
 > model-edit.pdb

 Chain information for FNV-E-prediction-1-best-model-edit.pdb #4
 ---
 Chain | Description
 A | No description available


 > select add #4

 7449 atoms, 7530 bonds, 493 residues, 1 model selected

 > ui mousemode right "translate selected models"

 > view matrix models #4,1,0,0,-20.268,0,1,0,-48.587,0,0,1,13.227

 > ui mousemode right "rotate selected models"

 > view matrix models
 >
 #4,-0.99857,0.049338,0.020729,772.69,-0.032585,-0.86781,0.49583,519.1,0.042452,0.49445,0.86817,-150.72

 > ui mousemode right "translate selected models"

 > view matrix models
 >
 #4,-0.99857,0.049338,0.020729,789.19,-0.032585,-0.86781,0.49583,500.69,0.042452,0.49445,0.86817,-146.12

 > view matrix models
 >
 #4,-0.99857,0.049338,0.020729,790.53,-0.032585,-0.86781,0.49583,500.53,0.042452,0.49445,0.86817,-145.92

 > ui mousemode right "rotate selected models"

 > view matrix models
 >
 #4,-0.99885,0.040425,0.025861,791.66,-0.022372,-0.86901,0.4943,497.76,0.042455,0.49315,0.86891,-145.77

 > ui mousemode right "translate selected models"

 > ui tool show "Fit in Map"

 > fitmap #4 inMap #1

 Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#4) to map test-fnv-
 asu_box.ccp4 (#1) using 7449 atoms
 average map value = 0.1097, steps = 128
 shifted from previous position = 9.03
 rotated from previous position = 15.1 degrees
 atoms outside contour = 3535, contour level = 0.107

 Position of FNV-E-prediction-1-best-model-edit.pdb (#4) relative to test-
 fnv-
 asu_box.ccp4 (#1) coordinates:
 Matrix rotation and translation
 -0.97725858 0.02825152 0.21016072 679.12240517
 0.04060965 -0.94780665 0.31624897 609.72599973
 0.20812624 0.31759157 0.92510489 -174.14668121
 Axis 0.10658756 0.16151476 0.98109738
 Axis point 348.04241714 320.28749895 0.00000000
 Rotation angle (degrees) 179.63914225
 Shift along axis 0.01089425


 > select subtract #4

 Nothing selected

 > select add #3

 7449 atoms, 7530 bonds, 493 residues, 1 model selected

 > view matrix models #3,1,0,0,32.528,0,1,0,-10.989,0,0,1,4.6657

 > ui mousemode right "rotate selected models"

 > view matrix models
 >
 #3,-0.9561,-0.073497,-0.28369,1044.2,0.075903,-0.99711,0.0025182,863.07,-0.28305,-0.019125,0.95891,154.94

 > view matrix models
 >
 #3,-0.94178,-0.08722,-0.32471,1068.9,0.063398,-0.99451,0.083256,819.18,-0.33019,0.057824,0.94214,149.46

 > ui mousemode right "translate selected models"

 > view matrix models
 >
 #3,-0.94178,-0.08722,-0.32471,1068,0.063398,-0.99451,0.083256,803.24,-0.33019,0.057824,0.94214,149.27

 > fitmap #3 inMap #1

 Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#3) to map test-fnv-
 asu_box.ccp4 (#1) using 7449 atoms
 average map value = 0.1057, steps = 224
 shifted from previous position = 3.16
 rotated from previous position = 55.2 degrees
 atoms outside contour = 3805, contour level = 0.107

 Position of FNV-E-prediction-1-best-model-edit.pdb (#3) relative to test-
 fnv-
 asu_box.ccp4 (#1) coordinates:
 Matrix rotation and translation
 -0.91036793 0.12790971 0.39353442 524.69773237
 0.14183002 -0.79696794 0.58713401 377.91727979
 0.38873446 0.59032296 0.70739262 -250.71847076
 Axis 0.21166597 0.31859580 0.92395575
 Axis point 290.29657732 233.25421562 -0.00000000
 Rotation angle (degrees) 179.56838716
 Shift along axis -0.18925892


 > view matrix models
 >
 #3,-0.91037,0.12791,0.39353,524.11,0.14183,-0.79697,0.58713,376.06,0.38873,0.59032,0.70739,-250.55

 > view matrix models
 >
 #3,-0.91037,0.12791,0.39353,524.12,0.14183,-0.79697,0.58713,376.12,0.38873,0.59032,0.70739,-250.55

 > fitmap #3 inMap #1

 Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#3) to map test-fnv-
 asu_box.ccp4 (#1) using 7449 atoms
 average map value = 0.1057, steps = 52
 shifted from previous position = 1.91
 rotated from previous position = 0.0252 degrees
 atoms outside contour = 3806, contour level = 0.107

 Position of FNV-E-prediction-1-best-model-edit.pdb (#3) relative to test-
 fnv-
 asu_box.ccp4 (#1) coordinates:
 Matrix rotation and translation
 -0.91035553 0.12831748 0.39343034 524.59477571
 0.14143086 -0.79699351 0.58719559 378.06830941
 0.38890889 0.59019994 0.70739939 -250.74625657
 Axis 0.21168422 0.31857800 0.92395771
 Axis point 290.29507266 233.26980806 0.00000000
 Rotation angle (degrees) 179.59340820
 Shift along axis -0.18625781


 > ui mousemode right select

 > select clear

 > view orient

 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainA-
 > edit.pdb models #4 relModel #1

 > view orient

 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainC-
 > edit.pdb models #2 relModel #1

 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainE-
 > edit.pdb models #3 relModel #1

 > close session

 > set bgColor white

 > open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4

 Opened test-fnv-asu_box.ccp4 as #1, grid size 81,145,67, pixel 1.33, shown
 at
 level 0.168, step 1, values float32

 > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 asu.pdb

 Chain information for 020223-FNV-alphafold-asu.pdb #2
 ---
 Chain | Description
 A C E | No description available
 B D F | No description available


 > hide atoms

 > style stick

 Changed 25200 atom styles

 > style stick

 Changed 25200 atom styles

 > show atoms

 > show cartoons

 > hide atoms

 > volume #1 level 0.1108

 > transparency 50

 > isolde start

 > set selectionWidth 4

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 Chain information for 020223-FNV-alphafold-asu.pdb
 ---
 Chain | Description
 2.2/A 2.2/C 2.2/E | No description available
 2.2/B 2.2/D 2.2/F | No description available

 ISOLDE: created disulfide bonds between the following residues:
 E92-E116; A92-A116; A74-A105; C3-C30; E3-E30; C60-C121; A3-A30; A300-A330;
 C74-C105; C300-C330; A182-A283; C92-C116; E60-E121; E300-E330; E74-E105;
 C182-C283; A60-A121; E182-E283

 > clipper associate #1 toModel #2

 Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33,
 shown at step 1, values float32

 > volume #2.1.1.1 level 0.09739

 > select add #2.2

 25200 atoms, 25473 bonds, 1653 residues, 6 models selected

 > addh

 Summary of feedback from adding hydrogens to 020223-FNV-alphafold-asu.pdb
 #2.2
 ---
 notes | No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2)
 chain
 A; guessing termini instead
 No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain B;
 guessing termini instead
 No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain C;
 guessing termini instead
 No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain D;
 guessing termini instead
 No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain E;
 guessing termini instead
 1 messages similar to the above omitted
 Chain-initial residues that are actual N termini: /A ALA 1, /C ALA 1, /E
 ALA 1
 Chain-initial residues that are not actual N termini: /B LYS 18, /D LYS
 18, /F
 LYS 18
 Chain-final residues that are actual C termini: /A ALA 493, /C ALA 493, /E
 ALA
 493
 Chain-final residues that are not actual C termini: /B SER 75, /D SER 75,
 /F
 SER 75
 1432 hydrogen bonds
 /B SER 75 is not terminus, removing H atom from 'C'
 /D SER 75 is not terminus, removing H atom from 'C'
 /F SER 75 is not terminus, removing H atom from 'C'
 0 hydrogens added


 > ui tool show "Ramachandran Plot"

 Traceback (most recent call last):
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/cbook/__init__.py", line 287, in process
 func(*args, **kwargs)
 File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
 on_resize
 c.draw()
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/backends/backend_agg.py", line 436, in draw
 self.figure.draw(self.renderer)
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/artist.py", line 73, in draw_wrapper
 result = draw(artist, renderer, *args, **kwargs)
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/artist.py", line 50, in draw_wrapper
 return draw(artist, renderer)
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/figure.py", line 2796, in draw
 artists = self._get_draw_artists(renderer)
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/figure.py", line 238, in _get_draw_artists
 ax.apply_aspect()
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect
 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)
 File
 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect
 raise ValueError("'box_aspect' and 'fig_aspect' must be positive")
 ValueError: 'box_aspect' and 'fig_aspect' must be positive

 > isolde sim start sel

 ISOLDE: started sim

 > isolde sim stop discardTo start

 reverting to start
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > isolde sim start sel

 ISOLDE: started sim

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 asu.cxs

 [Repeated 1 time(s)]

 ——— End of log from Thu Feb 2 16:14:31 2023 ———

 opened ChimeraX session

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 asu.cxs

 ——— End of log from Tue Feb 7 14:18:19 2023 ———

 opened ChimeraX session

 > close session

 > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 asu.pdb

 Chain information for 020223-FNV-alphafold-asu.pdb #1
 ---
 Chain | Description
 A C E | No description available
 B D F | No description available


 > style stick

 Changed 25011 atom styles

 > show cartoons

 > hide atoms

 > open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4

 Opened test-fnv-asu_box.ccp4 as #2, grid size 81,145,67, pixel 1.33, shown
 at
 level 0.168, step 1, values float32

 > volume #2 level 0.1034

 > transparency 50

 > isolde start

 > set selectionWidth 4

 Populating font family aliases took 156 ms. Replace uses of missing font
 family "Carlito" with one that exists to avoid this cost.

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 Chain information for 020223-FNV-alphafold-asu.pdb
 ---
 Chain | Description
 1.2/A 1.2/C 1.2/E | No description available
 1.2/B 1.2/D 1.2/F | No description available

 ISOLDE: created disulfide bonds between the following residues:
 A60-A121; A74-A105; C74-C105; C92-C116; A3-A30; C300-C330; C182-C283;
 E74-E105; E182-E283; E92-E116; A300-A330; C3-C30; E3-E30; E300-E330;
 A92-A116;
 C60-C121; A182-A283; E60-E121

 > clipper associate #2 toModel #1

 Opened test-fnv-asu_box.ccp4 as #1.1.1.1, grid size 81,145,67, pixel 1.33,
 shown at step 1, values float32

 > volume #1.1.1.1 level 0.1058

 > ui tool show "Ramachandran Plot"

 > isolde sim start sel

 ISOLDE: started sim

 > isolde sim stop discardTo start

 reverting to start
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > isolde sim start sel

 ISOLDE: started sim

 > isolde sim stop discardTo start

 reverting to start
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > volume #1.1.1.1 style surface

 > transparency 50

 > select clear

 > show cartoons

 [Repeated 1 time(s)]

 > hide atoms

 > ui tool show "Ramachandran Plot"

 > volume #1.1.1.1 level 0.09391

 > show sel atoms

 > select clear

 > select add #1.2

 25011 atoms, 25278 bonds, 1644 residues, 11 models selected

 > show sel atoms

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > volume #1.1.1.1 level 0.08533

 > select clear

 [Repeated 1 time(s)]

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > select clear

 [Repeated 3 time(s)]

 > isolde sim start sel

 ISOLDE: started sim

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-
 IUB
 standards.
 ISOLDE: stopped sim

 > isolde sim start sel

 ISOLDE: started sim

 > isolde sim stop discardTo start

 reverting to start
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > select clear

 > select #1.2/A:201

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

 > isolde sim start sel

 ISOLDE: started sim

 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
 bonded heavy atom.

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-
 IUB
 standards.
 ISOLDE: stopped sim

 > select clear

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > isolde sim start sel

 ISOLDE: started sim

 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
 bonded heavy atom.

 [Repeated 1 time(s)]

 > isolde sim stop discardTo start

 reverting to start
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > isolde sim start sel

 ISOLDE: started sim

 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
 bonded heavy atom.

 > isolde sim stop discardTo start

 reverting to start
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > select clear

 > isolde sim start sel

 ISOLDE: started sim

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-
 IUB
 standards.
 ISOLDE: stopped sim

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > select clear

 [Repeated 1 time(s)]

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > select clear

 [Repeated 2 time(s)]

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > select clear

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-
 > asu-1.cxs

 Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb

 > isolde cisflip #1.2/A:329

 Performing cis<\-->trans flip for 1 residues
 ISOLDE: started sim

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > isolde cisflip #1.2/E:329

 Performing cis<\-->trans flip for 1 residues
 ISOLDE: started sim

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > isolde cisflip #1.2/C:329

 Performing cis<\-->trans flip for 1 residues
 ISOLDE: started sim

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > isolde cisflip #1.2/C:329

 Performing cis<\-->trans flip for 1 residues
 ISOLDE: started sim

 > isolde sim stop discardTo start

 reverting to start
 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > view orient

 > select add #1.2

 25011 atoms, 25278 bonds, 1644 residues, 11 models selected

 > isolde pepflip sel

 Flipping the peptide bond for 1 residues
 ISOLDE: started sim

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > isolde sim start sel

 ISOLDE: started sim

 > ui mousemode right "isolde tug residue"

 > isolde sim stop

 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
 chains...
 ISOLDE: stopped sim

 > select clear

 > volume #1.1.1.1 level 0.09105

 > volume #1.1.1.1 level 0.09534

 Traceback (most recent call last):
 File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343,
 in
 _load_pae_from_file
 run(self.session,f'alphafold pae #{self._current_reference.id_string} file
 "{selected_file}" plot false')
 AttributeError: 'NoneType' object has no attribute 'id_string'

 AttributeError: 'NoneType' object has no attribute 'id_string'

 File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343,
 in
 _load_pae_from_file
 run(self.session,f'alphafold pae #{self._current_reference.id_string} file
 "{selected_file}" plot false')

 See log for complete Python traceback.

 Traceback (most recent call last):
 File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343,
 in
 _load_pae_from_file
 run(self.session,f'alphafold pae #{self._current_reference.id_string} file
 "{selected_file}" plot false')
 AttributeError: 'NoneType' object has no attribute 'id_string'

 AttributeError: 'NoneType' object has no attribute 'id_string'

 File "/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site-
 packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 343,
 in
 _load_pae_from_file
 run(self.session,f'alphafold pae #{self._current_reference.id_string} file
 "{selected_file}" plot false')

 See log for complete Python traceback.





 OpenGL version: 4.1 Metal - 83
 OpenGL renderer: Apple M1 Pro
 OpenGL vendor: Apple

 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: MacBookPro18,1
       Model Number: MK193LL/A
       Chip: Unknown
       Total Number of Cores: 10 (8 performance and 2 efficiency)
       Memory: 16 GB
       System Firmware Version: 8419.60.44
       OS Loader Version: 8419.60.44

 Software:

     System Software Overview:

       System Version: macOS 13.1 (22C65)
       Kernel Version: Darwin 22.2.0
       Time since boot: 4 hours, 25 minutes

 Graphics/Displays:

     Apple M1 Pro:

       Chipset Model: Apple M1 Pro
       Type: GPU
       Bus: Built-In
       Total Number of Cores: 16
       Vendor: Apple (0x106b)
       Metal Support: Metal 3
       Displays:
         Color LCD:
           Display Type: Built-in Liquid Retina XDR Display
           Resolution: 3456 x 2234 Retina
           Main Display: Yes
           Mirror: Off
           Online: Yes
           Automatically Adjust Brightness: Yes
           Connection Type: Internal


 Installed Packages:
     alabaster: 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-Clipper: 0.18.0
     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-ISOLDE: 1.4
     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

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8460>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  3 ; comment:3 by Tristan Croll, 3 years ago 

Even so, that shouldn’t be leading to a traceback. Will fix - thanks for
reporting it.

On Wed, 8 Feb 2023 at 19:37, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
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