mlp error: ValueError: list.remove(x): x not in list

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-05)
Description
Got a traceback after using Hydrophobic coloring icon.  Did not seem t produce an error dialog, just a traceback in the log.

Log:
UCSF ChimeraX version: 0.91 (2019-09-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6h6b format mmCIF fromDatabase pdb

6h6b title:  
Structure of alpha-synuclein fibrils [more info...]  
  
Chain information for 6h6b #1  
---  
Chain | Description  
A B C D E F G H I J | Alpha-synuclein  
  
  

> hide atoms

> show cartoons

> set bgColor white

> lighting simple

> graphics silhouettes true

> save /Users/goddard/Desktop/image1.png supersample 3

> close

> open 6h6b format mmCIF fromDatabase pdb

6h6b title:  
Structure of alpha-synuclein fibrils [more info...]  
  
Chain information for 6h6b #1  
---  
Chain | Description  
A B C D E F G H I J | Alpha-synuclein  
  
  

> save /Users/goddard/Desktop/image1.png supersample 3

> hide atoms

> show ribbons

> save /Users/goddard/Desktop/image1.png supersample 3

> show /A only

> show /A ribbons only

> hide /A

> show ribbons

> show /A ribbons only

> show ribbons

> save /Users/goddard/Desktop/image1.png supersample 3

> select clear

> color /D,E,F,I,J tan

> color /A,B,C,G,H pink

> save /Users/goddard/Desktop/image1.png supersample 3

> select /A

806 atoms, 808 bonds, 1 model selected  

> show /A ribbons only

> select clear

> save /Users/goddard/Desktop/image1.png supersample 3

> show /A atoms

> style stick

Changed 8060 atom styles  

> color byhetero

> save /Users/goddard/Desktop/image1.png supersample 3

> log metadata #1

Metadata for 6h6b #1  
---  
Title | Structure of alpha-synuclein fibrils  
Citation | Guerrero-Ferreira, R., Taylor, N.M., Mona, D., Ringler, P., Lauer,
M.E., Riek, R., Britschgi, M., Stahlberg, H. (2018). Cryo-EM structure of
alpha-synuclein fibrils. Elife, 7. PMID: 29969391. DOI: 10.7554/eLife.36402  
Gene source | Homo sapiens  
Experimental method | Electron microscopy  
Resolution | 3.4Å  
  
> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  

> select clear

> color sel orange

> color /D,E,F,I,J tan

> color /A,B,C,G,H pink

> color byhetero

> select clear

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1666, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 549, in close_request  
tool_instance.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.alignment.detach_viewer(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment  
alignment._destroy()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
KeyError: <chimerax.atomic.molobject.Chain object at 0x129c06550>  
  
KeyError:  
  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
  
See log for complete Python traceback.  
  

> save /Users/goddard/Desktop/seqbug.cxs

> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1666, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 549, in close_request  
tool_instance.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.alignment.detach_viewer(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment  
alignment._destroy()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
KeyError: <chimerax.atomic.molobject.Chain object at 0x129c06550>  
  
KeyError:  
  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
  
See log for complete Python traceback.  
  

> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  

> select clear

> select /A:52

16 atoms, 15 bonds, 1 model selected  

> select up

144 atoms, 144 bonds, 1 model selected  

> graphics selection width 4

> save /Users/goddard/Desktop/image1.png supersample 3

> select clear

> select strand

3540 atoms, 3500 bonds, 1 model selected  

> select clear

> label /A

> label height 1.4

> hide atoms

> show /A

> graphics silhouettes false

> hide H

> save /Users/goddard/Desktop/image1.png supersample 3

> save /Users/goddard/Desktop/image1.png supersample 3

> usage label

label [objects] [objectType] [text text] [offset offset] [color color]
[bgColor bgColor] [size size] [height height] [font a text string] [onTop true
or false]  
— Create atom labels  
objects: an objects specifier or nothing  
objectType: one of atoms, bonds, pseudobonds, or residues  
text: default or a text string  
offset: default or some numbers  
color: default or a color  
bgColor: none or a color  
size: default or an integer  
height: fixed or a number

label delete [objects] [objectType]  
— Delete atom labels  
objects: an objects specifier or nothing  
objectType: one of atoms, bonds, pseudobonds, or residues

label listfonts  
— List available fonts

label orient [orient]  
— Set label orientation updating  
orient: a number  

> label delete

> cofr

Center of rotation: 121.58 120.4 94.561 front center  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1666, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 549, in close_request  
tool_instance.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.alignment.detach_viewer(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment  
alignment._destroy()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
KeyError: <chimerax.atomic.molobject.Chain object at 0x129c06550>  
  
KeyError:  
  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
  
See log for complete Python traceback.  
  

> cofr frontCenter

> show ribbons

> lighting simple

> graphics silhouettes true

> hbonds

295 hydrogen bonds found  

> hide atoms

> save /Users/goddard/Desktop/image1.png supersample 3

> ~hbonds

> usage hbonds

hbonds [atoms] [makePseudobonds true or false] [radius a number] [color a
color] [showDist true or false] [restrict restrict] [interSubmodel true or
false] [interModel true or false] [intraModel true or false] [intraMol true or
false] [intraRes true or false] [cacheDa a number] [relax true or false]
[distSlop a number] [angleSlop a number] [twoColors true or false] [slopColor
a color] [reveal true or false] [retainCurrent true or false] [saveFile name
of a file to save/write] [log true or false] [namingStyle namingStyle] [batch
true or false] [dashes dashes] [saltOnly true or false] [name a text string]
[coordsets true or false]  
— Find hydrogen bonds  
atoms: an atoms specifier or nothing  
restrict: one of any, both, or cross or an atoms specifier  
namingStyle: one of command, serial, or simple  
dashes: an integer ≥ 0  

> usage ~hbonds

~hbonds [name a text string]  
— Clear hydrogen bonds  

> show surfaces

> lighting soft

> lighting full

> save /Users/goddard/Desktop/image1.png supersample 3

> color bfactor

8060 atoms, 580 residues, 10 surfaces, atom bfactor range 19.1 to 60.1  

> mlp

Map values for surface "6h6b_A SES surface": minimum -28.32, mean -4.205,
maximum 22.28  
Map values for surface "6h6b_B SES surface": minimum -28.29, mean -4.234,
maximum 22.78  
Map values for surface "6h6b_C SES surface": minimum -28.69, mean -4.206,
maximum 22.63  
Map values for surface "6h6b_D SES surface": minimum -28.48, mean -4.227,
maximum 22.65  
Map values for surface "6h6b_E SES surface": minimum -28.67, mean -4.197,
maximum 22.18  
Map values for surface "6h6b_F SES surface": minimum -28.2, mean -4.217,
maximum 22.35  
Map values for surface "6h6b_G SES surface": minimum -27.92, mean -4.26,
maximum 23.73  
Map values for surface "6h6b_H SES surface": minimum -28.31, mean -4.211,
maximum 22.08  
Map values for surface "6h6b_I SES surface": minimum -28.39, mean -4.225,
maximum 23.02  
Map values for surface "6h6b_J SES surface": minimum -28.76, mean -4.2,
maximum 22.47  
Exception ignored in: <function Drawing.__del__ at 0x1027124d0>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1113, in __del__  
self.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1700, in delete  
Model.delete(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 80, in delete  
Drawing.delete(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1129, in delete  
self.remove_all_drawings()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 318, in remove_all_drawings  
self.remove_drawings(cd, delete)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 311, in remove_drawings  
d.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1867, in delete  
self.volume._surfaces.remove(self)  
ValueError: list.remove(x): x not in list  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

Fixed I think. Could not reproduce.

The mlp command created volume contour surfaces due to an error in the code. Then deleting the volume surfaces modified the surface list while it was being looped over.