Volume Eraser: output array is read-only

[jmreimer@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-24)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-08-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-Rick/mini-RSC-
paper/Figures/Acidic_Patch/AP_A.cxs"

opened ChimeraX session  

> open "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-Rick/mini-RSC-
paper/Figures/Figure_3/LANA_peptide_overlay3.py"

ChimeraX cannot open a regular Chimera session.  
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.  

> open /Users/janicereimer/Documents/UCSD/RSC/mini-
RSC_paper/Figure3/Arg_acidic_patch.pdb

Chain information for Arg_acidic_patch.pdb #3  
---  
Chain | Description  
K | No description available  
L | No description available  
N | No description available  
X | No description available  
  

> hide #!3 models

> show #!3 models

> open "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-Rick/mini-RSC-
paper/Structures/Model_3-one-Sth1-MultiBody/model3-one-copy_20191002.pdb"

Chain information for model3-one-copy_20191002.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C G | No description available  
D H | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
  

> hide #!2 models

> hide #!1 models

> close #3

> open /Users/janicereimer/Documents/UCSD/RSC/mini-
RSC_paper/Figure3/Arg_acidic_patch.pdb

Chain information for Arg_acidic_patch.pdb #3  
---  
Chain | Description  
K | No description available  
L | No description available  
N | No description available  
X | No description available  
  

> close #3

> open /Users/janicereimer/Documents/UCSD/RSC/mini-
RSC_paper/Figure3/Arg_acidic_patch.pdb

Chain information for Arg_acidic_patch.pdb #3  
---  
Chain | Description  
K | No description available  
L | No description available  
N | No description available  
X | No description available  
  

> close #3

> open "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-Rick/mini-RSC-
paper/Figures/Acidic_Patch/arg_acidic_path2.pdb"

Chain information for arg_acidic_path2.pdb #3  
---  
Chain | Description  
K | No description available  
L | No description available  
N | No description available  
X | No description available  
  

> hide #!4 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #3/N green target c

> show #!1 models

> show #!2 models

> color #3/K red target c

> rainbow #3

> color #3 bychain

> color #3 bychain

> color #3/K crimson target c

> color #3/K "light coral" target c

> color #3/N "spring green" target c

> hide #!2 models

> hide #!1 models

> color #3/L gold target c

> color #3/X magenta target c

> color #3/K "hot pink" target c

> color #3/X "dark turquoise" target c

> color #3/K:1-16 "dark turquoise" target c

> color #3/K:1-17 "orange red" target c

> color #3/N "spring green" target c

Unknown command: color #3/K hot pink target c  

Unknown command: color #3/L gold target c  

Unknown command: color #3/X orange red target c  

Unknown command: color #3/K:1-17 cyan target  

Invalid "target" argument: Character 't' is not an allowed target, must be one
of acrsbpfl  

> color #3/X "orange red" target c

> color #3/K:1-17 cyan target c

> show #!1 models

> show #!2 models

> color #3 byhetero

> nucleotides #3 tube/slab shape box

> nucleotides #3 tube/slab shape box

> nucleotides #3 tube/slab shape box

> nucleotides #3 atoms

> style nucleic & #3 stick

Changed 0 atom styles  

> style #3 ball

Changed 626 atom styles  

> style #3 sphere

Changed 626 atom styles  

> style #3 stick

Changed 626 atom styles  

> style #3 sphere

Changed 626 atom styles  

> show #3 cartoons

> hide #3 cartoons

> show #3 cartoons

> show #3 surfaces

> hide #!3 surfaces

> style #!3 stick

Changed 626 atom styles  

> style #!3 sphere

Changed 626 atom styles  

> hide #!3 cartoons

> style #!3 stick

Changed 626 atom styles  

> style #!3 sphere

Changed 626 atom styles  

> style #!3 ball

Changed 626 atom styles  

> show #!3 atoms

> style #!3 ball

Changed 626 atom styles  

> style #!3 sphere

Changed 626 atom styles  

> nucleotides #!3 atoms

> style nucleic & #!3 stick

Changed 0 atom styles  

> nucleotides #!3 tube/slab shape box

> show #!3 atoms

> hide #!3 atoms

> show #!3 cartoons

> show #!3 cartoons

> style #!3 sphere

Changed 626 atom styles  

> show #!3 cartoons

> show #!3 atoms

> hide #!3 atoms

> show #!3 surfaces

> show #!3 surfaces

> hide #!3 surfaces

> show #!3 surfaces

> hide #!3 surfaces

> save LANA_overlay_test.png width 1200 height 1100 transparentBackground true

> open "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-Rick/mini-RSC-
paper/Figures/Acidic_Patch/large_arg_overlay.pdb"

Chain information for large_arg_overlay.pdb #5  
---  
Chain | Description  
K | No description available  
L | No description available  
V | No description available  
W | No description available  
Y | No description available  
  

> hide #!3 models

> hide #5 atoms

> show #5 cartoons

> show #!3 models

> hide #!2 models

> hide #!1 models

> color #5/K gold target c

> color #5/L "spring green" target c

> color #5/Y cyan target c

> color #5/W "hot pink" target c

> close #5

> open "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-Rick/mini-RSC-
paper/Figures/Acidic_Patch/large_arg_overlay.pdb"

Chain information for large_arg_overlay.pdb #5  
---  
Chain | Description  
K | No description available  
L | No description available  
W | No description available  
X | No description available  
Y | No description available  
  

> hide #5#!3 surfaces

> hide #5#!3 surfaces

> hide #5#!3 surfaces

> hide #5#!3 cartoons

> hide #5#!3 atoms

> show #5#!3 cartoons

> color #5/K gold target c

> color #5/L "spring green" target c

> color #5/Y cyan target c

> color #5/W "hot pink" target c

> color #5/X "orange red" target c

> show #!1 models

> show #!2 models

Expected a models specifier or a keyword  

> save AP_interactome.png width 1200 height 1100 transparentBackground true

> save AP_interactome.png width 1200 height 1100 transparentBackground false

> save session "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-
Rick/mini-RSC-paper/Figures/Acidic_Patch/AP_C.cxs"

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #5 surfaces

> show #!5 surfaces

> hide #!5 surfaces

> nucleotides #!5 tube/slab shape box

> color #5/K "orange red" target c

> color #5/L "spring green" target c

> color #5/Y cyan target c

> color #5/W "hot pink" target c

> color #5/X gold target c

> color #5/K gold target c

> color #5/L "spring green" target c

> color #5/Y cyan target c

> color #5/W "hot pink" target c

> color #5/X "orange red" target c

> color #5/X "dark orange" target c

> color #5/X magenta target c

> color #5/X tomato target c

> save AP_interactome.png width 1200 height 1100 transparentBackground false

> color #3/N "spring green" target c

Unknown command: color #3/K hot pink target c  

Unknown command: color #3/L gold target c  

Unknown command: color #3/X tomato target c  

Unknown command: color #3/K:1-17 cyan target c  

> color #3/N "spring green" target c

Unknown command: color #3/K hot pink target c  

Unknown command: color #3/L gold target c  

Unknown command: color #3/X tomato target c  

Unknown command: color #3/K:1-17 cyan target c  

> hide #!5 models

> show #!3 models

> color #3/X tomato target c

> show #!3 atoms

> hide #!3 atoms

> save session "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-
Rick/mini-RSC-paper/Figures/Acidic_Patch/AP_D.cxs"

> hide #!2 models

> hide #!1 models

> select :ARG

2516 atoms, 2304 bonds, 3 models selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> style sel stick

Changed 2516 atom styles  

> hide sel atoms

> select clear

> select down

Nothing selected  

> show #!2 models

> show #!1 models

> select #4/G

823 atoms, 833 bonds, 1 model selected  

> hide #!2 models

> hide #!1 models

> select #4/K:9

Nothing selected  

> select #3/K:9

11 atoms, 10 bonds, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> select clear

> select #3/L:30

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select #3/L:29

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> select clear

> select #3/K:223

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> select clear

> select #3/N:98

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> select #3/X:717

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> select clear

> color #3/N "spring green" target a

> color #3/N "spring green" target b

> color #3/N "spring green" target p

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color byatom

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> color #3/X tomato target b

> color #3/X tomato target b halfbond false

> color #3/X tomato target a halfbond false

> color #3/X tomato target a halfbond true

> color #3/X byelement

> color #3/X tomato target a halfbond true

> color #3/X byhetero

> color #3/N "spring green" target a

Unknown command: color #3/K hot pink target a  

Unknown command: color #3/L gold target a  

Unknown command: color #3/X tomato target a  

Unknown command: color #3/K:1-17 cyan target a  

> color #3/L gold target a

> color #3/K:1-17 cyan target a

> color #3/K "hot pink" target a

> color #3 byhetero

> show #!2 models

> show #!1 models

> save session "/Users/janicereimer/Dropbox (Personal)/Andres-Janice-
Rick/mini-RSC-paper/Figures/Acidic_Patch/AP_D.cxs"

> toolshed show "Map Eraser"

Can only have one displayed volume when erasing  

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume erase #2 center 144.56,83.491,234.42 radius 60.204

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 308, in _erase_in_sphere  
self._erase()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 327, in _erase  
run(self.session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 24, in volume_erase  
_zero_data_in_sphere(v.data, cvol, radius)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
ValueError: output array is read-only  
  
ValueError: output array is read-only  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
  
See log for complete Python traceback.  
  

> volume erase #2 center 153.48,96.13,235.35 radius 44.718

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 308, in _erase_in_sphere  
self._erase()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 327, in _erase  
run(self.session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 24, in volume_erase  
_zero_data_in_sphere(v.data, cvol, radius)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
ValueError: output array is read-only  
  
ValueError: output array is read-only  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_eraser/eraser.py", line 41, in _zero_data_in_sphere  
subtract(dmatrix, mdmatrix, dmatrix)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Reported by Janice Reimer

[Tom Goddard]

This ChimeraX bug using Volume Eraser was fixed 3 months ago. Update to a current ChimeraX daily build to get this working.