surface coloring error after swapaa

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-04)
Description
Changing atom colors after swapaa with surface shown gives this error.

Log:
UCSF ChimeraX version: 0.91 (2019-09-04)  
© 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

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

> color ~/A,B,C,G,H tan

> show ~H

> style stick

Changed 8060 atom styles  

> color byhetero

> hide ~/I,G

> hide ~/I,G ribbons

> set bgColor white

> graphics silhouettes true

> color :46,50,51,53 yellow

> surface /I,G

> color :46,50,51,53 yellow

> lighting soft

> lighting full

> label :46,50,51,53

Invalid "size" argument: Expected 'default' or an integer  

> label :46,50,51,53 height 1.5

> label :46,50,51,53 height 2

> label :46,50,51,53 height 3

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

> color ~/A,B,C,G,H tan

> color :46,50,51,53 yellow

> label :46,50,51,53 height 2

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

> label :46,50,51,53 height 2.5

> label :46,50,51,53 height 2

> 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 :46,50,51,53 height 2.5

> label :46,50,51,53 height 3

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

> hide surfaces

> label delete

> swapaa /I,G:53 GLU

Using Dunbrack library  
/I ALA 53: phi -136.3, psi 131.6 trans  
/G ALA 53: phi -136.3, psi 131.6 trans  
Applying GLU rotamer (chi angles: -63.7 -179.7 25.5) to /I GLU 53  
Applying GLU rotamer (chi angles: 178.2 66.7 76.0) to /G GLU 53  

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

> swapaa /I,G:53 ALA

Using Dunbrack library  
Swapping /I GLU 53 to ALA  
  
Swapping /G GLU 53 to ALA  
  

> color :46,50,51,53 yellow

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/color.py", line 122, in color  
undo_state=undo_state)  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/color.py", line 334, in _set_surface_colors  
ns = color_surfaces_at_atoms(atoms, color, opacity=opacity)  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/color.py", line 1225, in
color_surfaces_at_atoms  
s.color_atom_patches(atoms, color, opacity, per_atom_colors)  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 391, in color_atom_patches  
self._update_atom_patch_colors(atoms, color, per_atom_colors)  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 409, in _update_atom_patch_colors  
apc[ai] = acolors  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 806 but corresponding boolean dimension is 800  
  
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 806 but corresponding boolean dimension is 800  
  
File "/Users/goddard/Desktop/ChimeraX Sep 4
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molsurf.py", line 409, in _update_atom_patch_colors  
apc[ai] = acolors  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

Fixed.

Tried to use remembered molecular surface atom patch colors after atoms had been deleted by swapaa.