[Chimera-users] mrc maps

Tom Goddard goddard at cgl.ucsf.edu
Fri Jun 29 11:30:10 PDT 2007

Hi Tatiana,

  If you want the (x,y,z) coordinates for the a connected piece of a 
contour surface you could use the "Color and Measure Surface Pieces" 
extension on the Chimera experimental features page (2nd from the bottom):



That extension allows you to colors and reports the volume and area of 
individual blobs chosen with the mouse.  You could add a small bit of 
Python code to that extension to print the surface coordinates.  For 
example, you could add

    for xyz in varray:
        print '%12.5f %12.5f %12.5f' % xyz

at the end of the color_and_measure() routine in PickBlobs/gui.py to 
print the blob surface vertex coordinates.  The printed results would go 
to the Chimera Reply Log dialog when you click on a blob.  Those 
coordinates could be saved to a file (cut and paste).  The triangles 
that make up the surface blob are described by tarray (N by 3) where 
each triple of integers defines the indices of the triangle vertices in 


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