[Chimera-users] Data of Slice display

Tom Goddard goddard at cgl.ucsf.edu
Wed Mar 19 12:52:13 PDT 2008

Hi Jason,

You can have Chimera print out the density map values used for the slice
display in the volume tracer dialog by adding a line to the Python code.
Edit file


to add "print values" after the interpolated_values() call:

values = data_region.interpolated_values(xyz_list, vertex_xform,
use_subregion = True)
print values

Use the same indentation for the "print values" line as the preceding
one since that is important in Python. If you restart Chimera and place
a marker on your virus map it will output the array of values to the
reply log which you can display with menu entry Favorites / Reply Log.
You can copy and paste the values from there.

If you just want slices along the x, y or z axes you could get the exact
values from the map (no interpolation) by setting the volume region
bounds (volume menu Features / Region bounds) to just include a 1
dimensional slice (for example x range 83 83 1, y range 97 97 1 --
ranges are <min> <max> <step>) then open the attached Python script that
will print the values for just that region.


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