vseries measure: No module named 'chimerax.core.measure'

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-09-10)
Description
Although I was trying to see if "vseries measure" could be used on a single (non-series) map, the error sounds like it would  also happen with an actual volume series.  Commands:
open 2gbp
molmap ligand 5
vseries measure #2

Log:
UCSF ChimeraX version: 0.8 (2018-09-10)  
How to cite UCSF ChimeraX  

open 2gbp format mmCIF fromDatabase pdb ↵

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more&nbspinfo...;]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

molmap ligand 5 ↵

vseries measure #2 ↵

Traceback (most recent call last):  
  File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/map/series/vseries_command.py", line 310, in vseries_measure  
    from chimerax.core.measure import inertia  
ModuleNotFoundError: No module named 'chimerax.core.measure'  
  

ModuleNotFoundError: No module named 'chimerax.core.measure'  
  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/map/series/vseries_command.py", line 310, in vseries_measure  
from chimerax.core.measure import inertia  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.36.19
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Tom Goddard]

vseries measure is broken because the "measure inertia" code has not been ported to ChimeraX. Will need to port the inertia code.

[Tom Goddard]

The measure inertia code is in hydra, and needs porting to ChimeraX.

[Tom Goddard]

Fixed.

Added measure inertia code.

[Elaine Meng]

Vseries measure (in Chimera) also assigns a frame number to the resulting markers for synchronized playbackwith vseries showMarkers option but that  is a separate ticket #891 that I assume is not yet done.  Will change ChimeraX documentation to say that “showMarkers” is not implemented, unless you tell me there is some way to associate markers with series frame numbers.

[goddard@…]

The vseries marker display capabilities have not been ported to ChimeraX yet.  It should not be too hard.  But in Chimera it was a bit of a hack where the marker/atom label contained the time series frame number, and maybe I will want to figure out something better.

[goddard@…]

Here is an example of vseries measure output on a series with 5 time points.

vseries measure #1

# Volume series measurements: cell15_0ch_0000stack_000000msec.tif
# n level x y z step distance volume area inertia ellipsoid size 
0 178.97 195.03 321.19 69.836 0 0 2.6752e+05 83264 153.81 46.283 21.784
1 178.97 193.55 390.12 65.9 69.054 69.054 2.5746e+05 85952 140.92 48.977 20.324
2 178.97 185.19 432.79 68.119 43.543 112.6 2.3305e+05 80000 130.68 54.066 23.353
3 178.97 206.22 403.33 68.074 36.193 148.79 2.1664e+05 78077 97.225 67.891 21.796
4 178.97 191.72 350.36 68.842 54.929 203.72 2.0995e+05 89187 134.05 47.149 20.975

[Elaine Meng]

I realize it is a dumb user error, so file as desired, but if the series is shown as “image” rather than isosurface (as when DICOM is first opened) “vseries measure” gives a traceback culminating in TypeError: 'NoneType' object is not iterable

[goddard@…]

Fixed.  Now gives a clear error message saying vseries measure requires surface style display since the threshold level is used for reported centroid, area, volume, and size values.