Error copying map with "volume scale" command

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-15)
Description
Ran volume scale #1 factor -1 and got this error.

Log:
UCSF ChimeraX version: 0.91 (2019-08-15)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8624 fromDatabase emdb

Summary of feedback from opening 8624 fetched from emdb  
---  
note | Fetching compressed map 8624 from
ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-8624/map/emd_8624.map.gz  
  
Opened emd_8624.map, grid size 210,210,210, pixel 1.03, shown at level 0.0317,
step 1, values float32  

> open 5uz9

5uz9 title:  
Cryo EM structure of anti-CRISPRs, AcrF1 and AcrF2, bound to type I-F crRNA-
guided CRISPR surveillance complex [more info...]  
  
Chain information for 5uz9  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | CRISPR-associated protein Csy1  
2.1/B 2.2/B 2.3/B 2.4/B 2.5/B | CRISPR-associated protein Csy2  
2.1/C 2.2/C 2.3/C 2.4/C 2.5/C 2.1/D 2.2/D 2.3/D 2.4/D 2.5/D 2.1/E 2.2/E 2.3/E
2.4/E 2.5/E 2.1/F 2.2/F 2.3/F 2.4/F 2.5/F 2.1/G 2.2/G 2.3/G 2.4/G 2.5/G 2.1/H
2.2/H 2.3/H 2.4/H 2.5/H | CRISPR-associated protein Csy3  
2.1/I 2.2/I 2.3/I 2.4/I 2.5/I 2.1/J 2.2/J 2.3/J 2.4/J 2.5/J | Anti-CRISPR
protein Acr30-35  
2.1/K 2.2/K 2.3/K 2.4/K 2.5/K | Anti-CRISPR protein 30  
2.1/L 2.2/L 2.3/L 2.4/L 2.5/L | CRISPR-associated endonuclease Cas6/Csy4  
2.1/M 2.2/M 2.3/M 2.4/M 2.5/M | crispr RNA (60-mer)  
  
  

> style stick

Changed 121820 atom styles  

> close

> open 8089 fromDatabase emdb

Summary of feedback from opening 8089 fetched from emdb  
---  
note | Fetching compressed map 8089 from
ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-8089/map/emd_8089.map.gz  
  
Opened emd_8089.map, grid size 406,410,170, pixel 7.36,7.36,7.36, shown at
level 67, step 2, values int8  

> ui mousemode rightMode "crop volume"

> volume #1 region 0,0,32,405,409,35

> volume #1 region 0,0,32,405,409,39

> ui mousemode rightMode "move planes"

> volume #1 region 0,0,18,405,409,25

> volume #1 region 0,0,18,405,409,25

> volume #1 region 0,0,81,405,409,88

> volume #1 region 0,0,67,405,409,74

> volume #1 region 0,0,39,405,409,46

> volume #1 region 0,0,32,405,409,39

> volume #1 region 0,0,40,405,409,47

> volume #1 capFaces false

> usage volume

volume [volumes] [style style] [show] [hide] [toggle] [level level] [rmsLevel
rmsLevel] [sdLevel sdLevel] [encloseVolume encloseVolume] [fastEncloseVolume
fastEncloseVolume] [color color] [brightness a number] [transparency a number]
[appearance appearance] [step map step] [region map region] [nameRegion a text
string] [expandSinglePlane true or false] [origin 1 or 3 floats] [originIndex
1 or 3 floats] [voxelSize 1 or 3 floats] [planes planes
x|y|z[,<start>[,<end>[,<increment>[,<depth>]]]]] [dumpHeader true or false]
[pickable true or false] [symmetry symmetry] [center center point]
[centerIndex 1 or 3 floats] [axis an axis vector] [coordinateSystem a
coordinate-system] [dataCacheSize a number] [showOnOpen true or false]
[voxelLimitForOpen a number] [showPlane true or false] [voxelLimitForPlane a
number] [showOutlineBox true or false] [outlineBoxRgb a color]
[limitVoxelCount true or false] [voxelLimit a number] [colorMode colorMode]
[colormapOnGpu true or false] [colormapSize an integer] [blendOnGpu true or
false] [projectionMode projectionMode] [planeSpacing planeSpacing]
[fullRegionOnGpu true or false] [btCorrection true or false]
[minimalTextureMemory true or false] [maximumIntensityProjection true or
false] [linearInterpolation true or false] [dimTransparency true or false]
[dimTransparentVoxels true or false] [smoothLines true or false] [meshLighting
true or false] [twoSidedLighting true or false] [flipNormals true or false]
[subdivideSurface true or false] [subdivisionLevels an integer]
[surfaceSmoothing true or false] [smoothingIterations an integer]
[smoothingFactor a number] [squareMesh true or false] [capFaces true or false]
[boxFaces true or false] [orthoplanes orthoplanes] [positionPlanes
positionPlanes] [calculateSurfaces true or false]  
— set volume model parameters, display style and colors  
style: one of image, mesh, solid, or surface  
level: some numbers, repeatable  
rmsLevel: some numbers, repeatable  
sdLevel: some numbers, repeatable  
encloseVolume: some numbers  
fastEncloseVolume: some numbers  
color: a color, repeatable  
appearance: one of Airways, Airways II, Black & White, Bone + Skin, Bone +
Skin II, CT_Bones, CT_Kidneys, CT_Liver, CT_Lungs, CT_Muscles, CT_Skin,
CT_Soft_Tissue, CT_Vessels, CT_w_Contrast, Dark Bone, Glossy, Glossy II, Gold
Bone, High Contrast, Low Contrast, Mid Contrast, No Shading, Pencil, Red on
White, Skin On Blue, Skin On Blue II, Soft, Soft + Skin, Soft + Skin II, Soft
+ Skin III, Soft On Blue, Soft on White, Standard, Vascular, Vascular II,
Vascular III, Vascular IV, Yellow Bone, or initial  
colorMode: one of auto12, auto16, auto4, auto8, l12, l16, l4, l8, la12, la16,
la4, la8, opaque12, opaque16, opaque4, opaque8, rgb12, rgb16, rgb4, rgb8,
rgba12, rgba16, rgba4, or rgba8  
projectionMode: one of 2d-x, 2d-xyz, 2d-y, 2d-z, 3d, or auto  
planeSpacing: one of max, mean, or min or a number  
orthoplanes: one of off, xy, xyz, xz, or yz  
positionPlanes: some integers  
Subcommands are:

  * volume add
  * volume bin
  * volume boxes
  * volume cover
  * volume erase
  * volume falloff
  * volume flatten
  * volume flip
  * volume fourier
  * volume gaussian
  * volume laplacian
  * volume localCorrelation
  * volume mask
  * volume maximum
  * volume median
  * volume minimum
  * volume morph
  * volume multiply
  * volume new
  * volume octant
  * volume ~octant
  * volume onesmask
  * volume permuteAxes
  * volume resample
  * volume ridges
  * volume scale
  * volume settings
  * volume splitbyzone
  * volume subtract
  * volume threshold
  * volume tile
  * volume unbend
  * volume unroll
  * volume unzone
  * volume zone

  

> volume scale #1 factor -1

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.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/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2682, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/filter/vopcommand.py", line 778, in volume_scale  
session = session)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/filter/scale.py", line 31, in scaled_volume  
sv.copy_settings_from(v, copy_thresholds = False)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 883, in copy_settings_from  
default_rgba = v.default_rgba  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 294, in set_parameters  
% (len(values), len(self.surfaces)))  
ValueError: Number of surface colors (1) does not match number of surfaces (0)  
  
ValueError: Number of surface colors (1) does not match number of surfaces (0)  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 294, in set_parameters  
% (len(values), len(self.surfaces)))  
  
See log for complete Python traceback.  
  




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

[Tom Goddard]

Fixed.

volume scale command copied volume colors but not threshold levels and destination map did not have any surfaces while source map had 1 surface so the number of colors did not match. Fixed code so copying colors does not apply if number of surfaces or image nodes differs.